// Dispatcher service for Crunch that submits containers to the slurm queue.
import (
+ "bytes"
"flag"
"fmt"
- "io"
- "io/ioutil"
- "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"
"log"
"math"
"os"
"os/exec"
"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
//
// 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() {
}
var (
- theConfig Config
- squeueUpdater Squeue
+ theConfig Config
+ sqCheck SqueueChecker
)
const defaultConfigPath = "/etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml"
"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:])
log.Printf("warning: Client credentials missing from config, so falling back on environment variables (deprecated).")
}
+ if *dumpConfig {
+ log.Fatal(config.DumpAndExit(theConfig))
+ }
+
arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Printf("Error making Arvados client: %v", err)
}
arv.Retries = 25
- squeueUpdater.StartMonitor(time.Duration(theConfig.PollPeriod))
- defer squeueUpdater.Done()
+ sqCheck = SqueueChecker{Period: time.Duration(theConfig.PollPeriod)}
+ defer sqCheck.Stop()
dispatcher := dispatch.Dispatcher{
Arv: arv,
RunContainer: run,
- PollInterval: time.Duration(theConfig.PollPeriod),
- DoneProcessing: make(chan struct{})}
+ PollPeriod: time.Duration(theConfig.PollPeriod),
+ MinRetryPeriod: time.Duration(theConfig.MinRetryPeriod),
+ }
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
- }
-
- return nil
+ return dispatcher.Run()
}
// sbatchCmd
}
}()
- // 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
- }
+ // 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)))
- stderrReader, stderrErr := cmd.StderrPipe()
- if stderrErr != nil {
- submitErr = fmt.Errorf("Error creating stderr pipe %v: %q", container.UUID, stderrErr)
- return
- }
+ var stdout, stderr bytes.Buffer
+ cmd.Stdout = &stdout
+ cmd.Stderr = &stderr
// 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 sbatch: %v", err)
- return
- }
-
- stdoutChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stdoutReader)
- stdoutReader.Close()
- stdoutChan <- b
- close(stdoutChan)
- }()
-
- stderrChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stderrReader)
- stderrReader.Close()
- 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
- io.WriteString(stdinWriter, execScript(append(crunchRunCommand, container.UUID)))
- stdinWriter.Close()
-
- stdoutMsg := <-stdoutChan
- stderrmsg := <-stderrChan
-
- err = cmd.Wait()
-
- if err != nil {
- submitErr = fmt.Errorf("Container submission failed: %v: %v (stderr: %q)", cmd.Args, err, stderrmsg)
- return
+ sqCheck.L.Lock()
+ defer sqCheck.L.Unlock()
+
+ log.Printf("exec sbatch %+q", cmd.Args)
+ err := cmd.Run()
+ 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)
}
-
- log.Printf("sbatch succeeded: %s", strings.TrimSpace(string(stdoutMsg)))
- return
}
// If the container is marked as Locked, check if it is already in the slurm
func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container arvados.Container, monitorDone *bool) {
submitted := false
for !*monitorDone {
- if squeueUpdater.CheckSqueue(container.UUID) {
+ if sqCheck.HasUUID(container.UUID) {
// Found in the queue, so continue monitoring
submitted = true
} else if container.State == dispatch.Locked && !submitted {
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)
-
- // Mutex between squeue sync and running sbatch or scancel.
- squeueUpdater.SlurmLock.Lock()
- cmd := scancelCmd(container)
- msg, err := cmd.CombinedOutput()
- squeueUpdater.SlurmLock.Unlock()
-
- if err != nil {
- log.Printf("Error stopping container %s with %v %v: %v %v",
- container.UUID, cmd.Path, cmd.Args, err, string(msg))
- if squeueUpdater.CheckSqueue(container.UUID) {
- log.Printf("Container %s is still in squeue after scancel.",
- container.UUID)
- continue
- }
- }
+ 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()
- err = dispatcher.UpdateState(container.UUID, dispatch.Cancelled)
+ if err != nil {
+ 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
projects / arvados.git / commitdiff