package main
import (
+ "bufio"
"flag"
"fmt"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "io"
+ "io/ioutil"
"log"
+ "math"
"os"
"os/exec"
"os/signal"
+ "strconv"
"sync"
"syscall"
"time"
"/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:])
}(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()
return nil
}
+type apiClientAuthorization struct {
+ UUID string `json:"uuid"`
+ APIToken string `json:"api_token"`
+}
+
+type apiClientAuthorizationList struct {
+ Items []apiClientAuthorization `json:"items"`
+}
+
// 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) {
- ticker := time.NewTicker(time.Duration(pollInterval) * time.Second)
+func runQueuedContainers(pollInterval, priorityPollInterval int, crunchRunCommand, finishCommand string) {
+ var auth apiClientAuthorization
+ err := arv.Call("GET", "api_client_authorizations", "", "current", nil, &auth)
+ if err != nil {
+ log.Printf("Error getting my token UUID: %v", err)
+ return
+ }
+ ticker := time.NewTicker(time.Duration(pollInterval) * time.Second)
for {
select {
case <-ticker.C:
- dispatchSlurm(priorityPollInterval, crunchRunCommand)
+ dispatchSlurm(auth, time.Duration(priorityPollInterval)*time.Second, crunchRunCommand, finishCommand)
case <-doneProcessing:
ticker.Stop()
return
// Container data
type Container struct {
- UUID string `json:"uuid"`
- State string `json:"state"`
- Priority int `json:"priority"`
+ UUID string `json:"uuid"`
+ State string `json:"state"`
+ Priority int `json:"priority"`
+ RuntimeConstraints map[string]int64 `json:"runtime_constraints"`
+ LockedByUUID string `json:"locked_by_uuid"`
}
// ContainerList is a list of the containers from api
Items []Container `json:"items"`
}
-// Get the list of queued containers from API server and invoke run for each container.
-func dispatchSlurm(priorityPollInterval int, crunchRunCommand string) {
+// Get the list of queued containers from API server and invoke run
+// for each container.
+func dispatchSlurm(auth apiClientAuthorization, pollInterval time.Duration, crunchRunCommand, finishCommand string) {
params := arvadosclient.Dict{
- "filters": [][]string{[]string{"state", "=", "Queued"}},
+ "filters": [][]interface{}{{"state", "in", []string{"Queued", "Locked"}}},
}
var containers ContainerList
return
}
- 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)
+ for _, container := range containers.Items {
+ if container.State == "Locked" {
+ if container.LockedByUUID != auth.UUID {
+ // Locked by a different dispatcher
+ continue
+ } else if checkMine(container.UUID) {
+ // I already have a goroutine running
+ // for this container: it just hasn't
+ // gotten past Locked state yet.
+ continue
+ }
+ log.Printf("WARNING: found container %s already locked by my token %s, but I didn't submit it. "+
+ "Assuming it was left behind by a previous dispatch process, and waiting for it to finish.",
+ container.UUID, auth.UUID)
+ setMine(container.UUID, true)
+ go func() {
+ waitContainer(container, pollInterval)
+ setMine(container.UUID, false)
+ }()
+ }
+ go run(container, crunchRunCommand, finishCommand, pollInterval)
}
}
-// 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()
+// 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"])))
+}
+
+var sbatchCmd = sbatchFunc
- 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)
+// 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
+
+ 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 := 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
}
- fmt.Fprintf(stdinWriter, "#!/bin/sh\nexec %s %s\n", crunchRunCommand, uuid)
+ 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
+ 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)
+ // BUG: we drop the error here and forget about it. A
+ // human has to notice the container is stuck in
+ // Running state, and fix it manually.
+ }
+}
+
+// Run a queued container: [1] Set container state to locked. [2]
+// Execute crunch-run as a slurm batch job. [3] waitContainer().
+func run(container Container, crunchRunCommand, finishCommand string, pollInterval time.Duration) {
+ setMine(container.UUID, true)
+ defer setMine(container.UUID, false)
+
+ // Update container status to Locked. This will fail if
+ // another dispatcher (token) has already locked it. It will
+ // succeed if *this* dispatcher has already locked it.
+ err := arv.Update("containers", container.UUID,
+ arvadosclient.Dict{
+ "container": arvadosclient.Dict{"state": "Locked"}},
+ nil)
+ if err != nil {
+ log.Printf("Error updating container state to 'Locked' for %v: %q", container.UUID, err)
+ return
+ }
+
+ log.Printf("About to submit queued container %v", container.UUID)
+
+ jobid, err := submit(container, crunchRunCommand)
+ if err != nil {
+ log.Printf("Error submitting container %s to slurm: %v", container.UUID, 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 will fail if
+ // another dispatcher (token) has already locked it. It will
+ // succeed if *this* dispatcher has already locked it.
+ 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 %v to slurm", container.UUID)
+ waitContainer(container, pollInterval)
+}
- log.Printf("Submitted container run for %v", uuid)
+// Wait for a container to finish. Cancel the slurm job if the
+// container priority changes to zero before it ends.
+func waitContainer(container Container, pollInterval time.Duration) {
+ log.Printf("Monitoring container %v started", container.UUID)
+ defer log.Printf("Monitoring container %v finished", 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)
- if err != nil {
- log.Printf("Error getting container info for %v: %q", uuid, err)
- } else {
- if container.Priority == 0 {
- priorityTicker.Stop()
- cancelcmd := exec.Command("scancel", "--name="+uuid)
- cancelcmd.Run()
- }
+ pollTicker := time.NewTicker(pollInterval)
+ defer pollTicker.Stop()
+ for _ = range pollTicker.C {
+ var updated Container
+ err := arv.Get("containers", container.UUID, nil, &updated)
+ if err != nil {
+ log.Printf("Error getting container %s: %q", container.UUID, err)
+ continue
+ }
+ if updated.State == "Complete" || updated.State == "Cancelled" {
+ return
+ }
+ if updated.Priority != 0 {
+ continue
+ }
+
+ // Priority is zero, but state is Running or Locked
+ 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 := checkSqueue(container.UUID); err != nil {
+ log.Printf("Error running squeue: %v", err)
+ continue
+ } else if inQ {
+ log.Printf("Container %s is still in squeue; will retry", container.UUID)
+ continue
}
}
- }()
+ err = arv.Update("containers", container.UUID,
+ arvadosclient.Dict{
+ "container": arvadosclient.Dict{"state": "Cancelled"}},
+ nil)
+ if err != nil {
+ log.Printf("Error updating state for container %s: %s", container.UUID, err)
+ continue
+ }
+
+ return
+ }
+}
+
+func checkSqueue(uuid string) (bool, error) {
+ cmd := exec.Command("squeue", "--format=%j")
+ sq, err := cmd.StdoutPipe()
+ if err != nil {
+ return false, err
+ }
+ cmd.Start()
+ defer cmd.Wait()
+ scanner := bufio.NewScanner(sq)
+ found := false
+ for scanner.Scan() {
+ if scanner.Text() == uuid {
+ found = true
+ }
+ }
+ if err := scanner.Err(); err != nil {
+ return false, err
+ }
+ return found, nil
+}
+
+var mineMutex sync.RWMutex
+var mineMap = make(map[string]bool)
+
+// Goroutine-safely add/remove uuid to the set of "my" containers,
+// i.e., ones for which this process has a goroutine running.
+func setMine(uuid string, t bool) {
+ mineMutex.Lock()
+ if t {
+ mineMap[uuid] = true
+ } else {
+ delete(mineMap, uuid)
+ }
+ mineMutex.Unlock()
+}
+
+// Check whether there is already a goroutine running for this
+// container.
+func checkMine(uuid string) bool {
+ mineMutex.RLocker().Lock()
+ defer mineMutex.RLocker().Unlock()
+ return mineMap[uuid]
}