X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3ae9a789410e93eeb31ca5670c17a6d03d77f608..8668135855b400e7f6047ecacd9cfa27fed723f7:/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 3e148203f1..3c4f281912 100644 --- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go +++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go @@ -3,55 +3,92 @@ package main // Dispatcher service for Crunch that submits containers to the slurm queue. import ( - "bufio" "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/config" "git.curoverse.com/arvados.git/sdk/go/dispatch" + "github.com/coreos/go-systemd/daemon" + "io" "io/ioutil" "log" "math" "os" "os/exec" "strings" - "sync" "time" ) -type Squeue struct { - sync.Mutex - squeueContents []string - SqueueDone chan struct{} +// 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 { - log.Fatalf("%q", err) + log.Fatal(err) } } var ( - crunchRunCommand *string - squeueUpdater Squeue + theConfig Config + squeueUpdater Squeue ) +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") - - crunchRunCommand = flags.String( - "crunch-run-command", - "/usr/bin/crunch-run", - "Crunch command to run container") + configPath := flags.String( + "config", + defaultConfigPath, + "`path` to JSON or YAML configuration file") // 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).") + } + arv, err := arvadosclient.MakeArvadosClient() if err != nil { log.Printf("Error making Arvados client: %v", err) @@ -59,50 +96,56 @@ func doMain() error { } arv.Retries = 25 + squeueUpdater.StartMonitor(time.Duration(theConfig.PollPeriod)) + defer squeueUpdater.Done() + dispatcher := dispatch.Dispatcher{ Arv: arv, RunContainer: run, - PollInterval: time.Duration(*pollInterval) * time.Second, + PollInterval: time.Duration(theConfig.PollPeriod), DoneProcessing: make(chan struct{})} - squeueUpdater.SqueueDone = make(chan struct{}) - go squeueUpdater.SyncSqueue(time.Duration(*pollInterval) * time.Second) + if _, err := daemon.SdNotify(false, "READY=1"); err != nil { + log.Printf("Error notifying init daemon: %v", err) + } err = dispatcher.RunDispatcher() if err != nil { return err } - squeueUpdater.SqueueDone <- struct{}{} - close(squeueUpdater.SqueueDone) - return nil } // 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, 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...) } -// squeueFunc -func squeueFunc() *exec.Cmd { - return exec.Command("squeue", "--format=%j") +// 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 squeueCmd = squeueFunc +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. @@ -110,10 +153,7 @@ 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) } @@ -139,9 +179,14 @@ func submit(dispatcher *dispatch.Dispatcher, return } + // Mutex between squeue sync and running sbatch or scancel. + squeueUpdater.SlurmLock.Lock() + defer squeueUpdater.SlurmLock.Unlock() + + log.Printf("sbatch starting: %+q", cmd.Args) err := cmd.Start() if err != nil { - submitErr = fmt.Errorf("Error starting %v: %v", cmd.Args, err) + submitErr = fmt.Errorf("Error starting sbatch: %v", err) return } @@ -161,7 +206,7 @@ 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() @@ -173,168 +218,97 @@ 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 } -func (squeue *Squeue) runSqueue() ([]string, error) { - var newSqueueContents []string - - cmd := squeueCmd() - sq, err := cmd.StdoutPipe() - if err != nil { - return nil, err - } - cmd.Start() - scanner := bufio.NewScanner(sq) - for scanner.Scan() { - newSqueueContents = append(newSqueueContents, scanner.Text()) - } - if err := scanner.Err(); err != nil { - cmd.Wait() - return nil, err - } - - err = cmd.Wait() - if err != nil { - return nil, err - } - - return newSqueueContents, nil -} - -func (squeue *Squeue) CheckSqueue(uuid string, check bool) (bool, error) { - if check { - n, err := squeue.runSqueue() - if err != nil { - return false, err - } - squeue.Lock() - squeue.squeueContents = n - squeue.Unlock() - } - - if uuid != "" { - squeue.Lock() - defer squeue.Unlock() - for _, k := range squeue.squeueContents { - if k == uuid { - return true, nil - } - } - } - return false, nil -} - -func (squeue *Squeue) SyncSqueue(pollInterval time.Duration) { - // TODO: considering using "squeue -i" instead of polling squeue. - ticker := time.NewTicker(pollInterval) - for { - select { - case <-squeueUpdater.SqueueDone: - return - case <-ticker.C: - squeue.CheckSqueue("", true) - } - } -} - -// Run or monitor a container. -// // 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. -// -// 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) { - - uuid := container.UUID +func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container arvados.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. - if container.State == dispatch.Locked { - if inQ, err := squeueUpdater.CheckSqueue(container.UUID, true); err != nil { - // maybe squeue is broken, put it back in the queue - log.Printf("Error running squeue: %v", err) - dispatcher.UpdateState(container.UUID, dispatch.Queued) - } else if !inQ { log.Printf("About to submit queued container %v", container.UUID) - if _, err := submit(dispatcher, container, *crunchRunCommand); err != nil { + 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.UpdateState(container.UUID, dispatch.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 } } } +} - log.Printf("Monitoring container %v started", uuid) - - // periodically check squeue - doneSqueue := make(chan struct{}) - go func() { - squeueUpdater.CheckSqueue(container.UUID, true) - ticker := time.NewTicker(dispatcher.PollInterval) - for { - select { - case <-ticker.C: - if inQ, err := squeueUpdater.CheckSqueue(container.UUID, false); err != nil { - log.Printf("Error running squeue: %v", err) - // don't cancel, just leave it the way it is - } else if !inQ { - var con dispatch.Container - err := dispatcher.Arv.Get("containers", uuid, nil, &con) - if err != nil { - log.Printf("Error getting final container state: %v", err) - } +// 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) { - var st string - switch con.State { - case dispatch.Locked: - st = dispatch.Queued - case dispatch.Running: - st = dispatch.Cancelled - default: - st = "" - } + log.Printf("Monitoring container %v started", container.UUID) + defer log.Printf("Monitoring container %v finished", container.UUID) - if st != "" { - log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.", - uuid, con.State, st) - dispatcher.UpdateState(uuid, st) - } - } - case <-doneSqueue: - close(doneSqueue) - ticker.Stop() - return - } - } - }() + 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) - err := exec.Command("scancel", "--name="+container.UUID).Run() + // 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 inQ, err := squeueUpdater.CheckSqueue(container.UUID, true); err != nil { - log.Printf("Error running squeue: %v", err) - continue - } else if inQ { + if squeueUpdater.CheckSqueue(container.UUID) { log.Printf("Container %s is still in squeue after scancel.", container.UUID) continue @@ -345,8 +319,14 @@ func run(dispatcher *dispatch.Dispatcher, } } } + monitorDone = true +} - doneSqueue <- struct{}{} - - log.Printf("Monitoring container %v finished", uuid) +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 }