X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5762dc9c58290f3c760b9183f6735d056c895daf..da6e931b990c7edde55213196fc8a47f4dc4998d:/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 29d58c528e..8fbc0fa8b6 100644 --- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go +++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go @@ -4,7 +4,7 @@ import ( "flag" "fmt" "git.curoverse.com/arvados.git/sdk/go/arvadosclient" - "io" + "io/ioutil" "log" "os" "os/exec" @@ -48,6 +48,11 @@ func doMain() error { "/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") + // Parse args; omit the first arg which is the command name flags.Parse(os.Args[1:]) @@ -71,7 +76,7 @@ func doMain() error { }(sigChan) // Run all queued containers - runQueuedContainers(*pollInterval, *priorityPollInterval, *crunchRunCommand) + runQueuedContainers(*pollInterval, *priorityPollInterval, *crunchRunCommand, *finishCommand) // Wait for all running crunch jobs to complete / terminate waitGroup.Wait() @@ -80,18 +85,18 @@ func doMain() error { } // Poll for queued containers using pollInterval. -// Invoke dispatchLocal for each ticker cycle, which will run all the queued containers. +// 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 string) { +func runQueuedContainers(pollInterval, priorityPollInterval int, crunchRunCommand, finishCommand string) { ticker := time.NewTicker(time.Duration(pollInterval) * time.Second) for { select { case <-ticker.C: - dispatchSlurm(priorityPollInterval, crunchRunCommand) + dispatchSlurm(priorityPollInterval, crunchRunCommand, finishCommand) case <-doneProcessing: ticker.Stop() return @@ -112,7 +117,7 @@ type ContainerList struct { } // Get the list of queued containers from API server and invoke run for each container. -func dispatchSlurm(priorityPollInterval int, crunchRunCommand string) { +func dispatchSlurm(priorityPollInterval int, crunchRunCommand, finishCommand string) { params := arvadosclient.Dict{ "filters": [][]string{[]string{"state", "=", "Queued"}}, } @@ -127,57 +132,167 @@ func dispatchSlurm(priorityPollInterval int, crunchRunCommand string) { 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].UUID, crunchRunCommand, priorityPollInterval) + go run(containers.Items[i], crunchRunCommand, finishCommand, priorityPollInterval) } } -// Run queued container: -// Set container state to locked (TBD) -// Run container using the given crunch-run command -// Set the container state to Running -// If the container priority becomes zero while crunch job is still running, terminate it. -func run(uuid string, crunchRunCommand string, priorityPollInterval int) { - stdinReader, stdinWriter := io.Pipe() - - cmd := exec.Command("sbatch", "--job-name="+uuid) - cmd.Stdin = stdinReader - cmd.Stderr = os.Stderr - cmd.Stdout = os.Stderr - if err := cmd.Start(); err != nil { - log.Printf("Error running container for %v: %q", uuid, err) +// sbatchCmd +func sbatchFunc(uuid string) *exec.Cmd { + return exec.Command("sbatch", "--job-name="+uuid, "--share", "--parsable") +} + +var sbatchCmd = sbatchFunc + +// 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)) +} + +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) + } + } + }() + + // 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 } - fmt.Fprintf(stdinWriter, "#!/bin/sh\nexec %s %s\n", crunchRunCommand, uuid) + 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() - cmd.Wait() - // Update container status to Running - err := arv.Update("containers", uuid, + err = cmd.Wait() + + stdoutMsg := <-stdoutChan + stderrmsg := <-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 = string(stdoutMsg) + + 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 + err := cmd.Run() + if err != nil { + log.Printf("While setting up strigger: %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 + } + + 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", uuid, err) + log.Printf("Error updating container state to 'Running' for %v: %q", container.UUID, err) } - log.Printf("Submitted container run for %v", uuid) + log.Printf("Submitted container run for %v", container.UUID) + + containerUUID := container.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", uuid, nil, &container) + err := arv.Get("containers", containerUUID, nil, &container) if err != nil { - log.Printf("Error getting container info for %v: %q", uuid, err) + 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="+uuid) + cancelcmd := exec.Command("scancel", "--name="+container.UUID) cancelcmd.Run() } + if container.State == "Complete" { + priorityTicker.Stop() + } } } }()