package main // Dispatcher service for Crunch that submits containers to the slurm queue. import ( "bufio" "flag" "fmt" "git.curoverse.com/arvados.git/sdk/go/arvadosclient" "git.curoverse.com/arvados.git/sdk/go/dispatch" "io/ioutil" "log" "math" "os" "os/exec" "strings" "sync" "time" ) type Squeue struct { sync.Mutex squeueContents []string SqueueDone chan struct{} } func main() { err := doMain() if err != nil { log.Fatalf("%q", err) } } var ( crunchRunCommand *string squeueUpdater Squeue ) func doMain() error { flags := flag.NewFlagSet("crunch-dispatch-slurm", flag.ExitOnError) 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") // Parse args; omit the first arg which is the command name flags.Parse(os.Args[1:]) arv, err := arvadosclient.MakeArvadosClient() if err != nil { log.Printf("Error making Arvados client: %v", err) return err } arv.Retries = 25 dispatcher := dispatch.Dispatcher{ Arv: arv, RunContainer: run, PollInterval: time.Duration(*pollInterval) * time.Second, DoneProcessing: make(chan struct{})} squeueUpdater.SqueueDone = make(chan struct{}) go squeueUpdater.SyncSqueue(time.Duration(*pollInterval) * time.Second) 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)) } // squeueFunc func squeueFunc() *exec.Cmd { return exec.Command("squeue", "--format=%j") } // Wrap these so that they can be overridden by tests var sbatchCmd = sbatchFunc var squeueCmd = squeueFunc // Submit job to slurm using sbatch. func submit(dispatcher *dispatch.Dispatcher, container dispatch.Container, crunchRunCommand string) (jobid string, submitErr error) { submitErr = nil 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 } err := dispatcher.Arv.Update("containers", container.UUID, arvadosclient.Dict{ "container": arvadosclient.Dict{"state": "Queued"}}, nil) if err != nil { log.Printf("Error unlocking container %s: %v", container.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 } 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) stdoutReader.Close() stdoutChan <- b }() stderrChan := make(chan []byte) go func() { b, _ := ioutil.ReadAll(stderrReader) stderrReader.Close() stderrChan <- b }() // 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 close(stdoutChan) close(stderrChan) if err != nil { submitErr = fmt.Errorf("Container submission failed %v: %v %v", cmd.Args, err, stderrmsg) return } // If everything worked out, got the jobid on stdout jobid = 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 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 { 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) } } } 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) } var st string switch con.State { case dispatch.Locked: st = dispatch.Queued case dispatch.Running: st = dispatch.Cancelled default: st = "" } 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 } } }() 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() 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 { log.Printf("Container %s is still in squeue after scancel.", container.UUID) continue } } err = dispatcher.UpdateState(container.UUID, dispatch.Cancelled) } } } doneSqueue <- struct{}{} log.Printf("Monitoring container %v finished", uuid) }