"os"
"os/exec"
"os/signal"
+ "os/user"
"path"
"path/filepath"
"regexp"
"time"
"git.arvados.org/arvados.git/lib/cmd"
+ "git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/crunchstat"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
+ "git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/keepclient"
"git.arvados.org/arvados.git/sdk/go/manifest"
+ "golang.org/x/sys/unix"
)
type command struct{}
enableMemoryLimit bool
enableNetwork string // one of "default" or "always"
networkMode string // "none", "host", or "" -- passed through to executor
+ brokenNodeHook string // script to run if node appears to be broken
arvMountLog *ThrottledLogger
containerWatchdogInterval time.Duration
"(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
"(?ms).*grpc: the connection is unavailable.*",
}
-var brokenNodeHook *string = flag.String("broken-node-hook", "", "Script to run if node is detected to be broken (for example, Docker daemon is not running)")
func (runner *ContainerRunner) runBrokenNodeHook() {
- if *brokenNodeHook == "" {
+ if runner.brokenNodeHook == "" {
path := filepath.Join(lockdir, brokenfile)
runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
}
f.Close()
} else {
- runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
+ runner.CrunchLog.Printf("Running broken node hook %q", runner.brokenNodeHook)
// run killme script
- c := exec.Command(*brokenNodeHook)
+ c := exec.Command(runner.brokenNodeHook)
c.Stdout = runner.CrunchLog
c.Stderr = runner.CrunchLog
err := c.Run()
"--storage-classes", strings.Join(runner.Container.OutputStorageClasses, ","),
fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
- if runner.executor.Runtime() == "docker" {
+ if _, isdocker := runner.executor.(*dockerExecutor); isdocker {
arvMountCmd = append(arvMountCmd, "--allow-other")
}
sort.Strings(binds)
for _, bind := range binds {
- mnt, ok := runner.Container.Mounts[bind]
- if !ok {
+ mnt, notSecret := runner.Container.Mounts[bind]
+ if !notSecret {
mnt = runner.SecretMounts[bind]
}
if bind == "stdout" || bind == "stderr" {
}
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
- arvMountCmd = append(arvMountCmd, "--mount-tmp")
- arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
+ arvMountCmd = append(arvMountCmd, "--mount-tmp", fmt.Sprintf("tmp%d", tmpcount))
tmpcount++
}
if mnt.Writable {
if err != nil {
return nil, fmt.Errorf("writing temp file: %v", err)
}
- if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
+ if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && (notSecret || runner.Container.Mounts[runner.Container.OutputPath].Kind != "collection") {
+ // In most cases, if the container
+ // specifies a literal file inside the
+ // output path, we copy it into the
+ // output directory (either a mounted
+ // collection or a staging area on the
+ // host fs). If it's a secret, it will
+ // be skipped when copying output from
+ // staging to Keep later.
copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
+ // If a secret is outside OutputPath,
+ // we bind mount the secret file
+ // directly just like other mounts. We
+ // also use this strategy when a
+ // secret is inside OutputPath but
+ // OutputPath is a live collection, to
+ // avoid writing the secret to
+ // Keep. Attempting to remove a
+ // bind-mounted secret file from
+ // inside the container will return a
+ // "Device or resource busy" error
+ // that might not be handled well by
+ // the container, which is why we
+ // don't use this strategy when
+ // OutputPath is a staging directory.
bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
}
}
if pdhOnly {
- arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
+ // If we are only mounting collections by pdh, make
+ // sure we don't subscribe to websocket events to
+ // avoid putting undesired load on the API server
+ arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id", "--disable-event-listening")
} else {
arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
}
+ // the by_uuid mount point is used by singularity when writing
+ // out docker images converted to SIF
arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_uuid")
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
runner.executorStdin = stdin
runner.executorStdout = stdout
runner.executorStderr = stderr
+
+ if runner.Container.RuntimeConstraints.CUDA.DeviceCount > 0 {
+ nvidiaModprobe(runner.CrunchLog)
+ }
+
return runner.executor.Create(containerSpec{
- Image: imageID,
- VCPUs: runner.Container.RuntimeConstraints.VCPUs,
- RAM: ram,
- WorkingDir: workdir,
- Env: env,
- BindMounts: bindmounts,
- Command: runner.Container.Command,
- EnableNetwork: enableNetwork,
- NetworkMode: runner.networkMode,
- CgroupParent: runner.setCgroupParent,
- Stdin: stdin,
- Stdout: stdout,
- Stderr: stderr,
+ Image: imageID,
+ VCPUs: runner.Container.RuntimeConstraints.VCPUs,
+ RAM: ram,
+ WorkingDir: workdir,
+ Env: env,
+ BindMounts: bindmounts,
+ Command: runner.Container.Command,
+ EnableNetwork: enableNetwork,
+ CUDADeviceCount: runner.Container.RuntimeConstraints.CUDA.DeviceCount,
+ NetworkMode: runner.networkMode,
+ CgroupParent: runner.setCgroupParent,
+ Stdin: stdin,
+ Stdout: stdout,
+ Stderr: stderr,
})
}
}
runner.ExitCode = &exitcode
+ extra := ""
+ if exitcode&0x80 != 0 {
+ // Convert raw exit status (0x80 + signal number) to a
+ // string to log after the code, like " (signal 101)"
+ // or " (signal 9, killed)"
+ sig := syscall.WaitStatus(exitcode).Signal()
+ if name := unix.SignalName(sig); name != "" {
+ extra = fmt.Sprintf(" (signal %d, %s)", sig, name)
+ } else {
+ extra = fmt.Sprintf(" (signal %d)", sig)
+ }
+ }
+ runner.CrunchLog.Printf("Container exited with status code %d%s", exitcode, extra)
+
var returnErr error
if err = runner.executorStdin.Close(); err != nil {
err = fmt.Errorf("error closing container stdin: %s", err)
// Run the full container lifecycle.
func (runner *ContainerRunner) Run() (err error) {
runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
- runner.CrunchLog.Printf("Executing container '%s' using %s runtime", runner.Container.UUID, runner.executor.Runtime())
+ runner.CrunchLog.Printf("%s", currentUserAndGroups())
+ v, _ := exec.Command("arv-mount", "--version").CombinedOutput()
+ runner.CrunchLog.Printf("Using FUSE mount: %s", v)
+ runner.CrunchLog.Printf("Using container runtime: %s", runner.executor.Runtime())
+ runner.CrunchLog.Printf("Executing container: %s", runner.Container.UUID)
hostname, hosterr := os.Hostname()
if hosterr != nil {
caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
stdinConfig := flags.Bool("stdin-config", false, "Load config and environment variables from JSON message on stdin")
+ configFile := flags.String("config", arvados.DefaultConfigFile, "filename of cluster config file to try loading if -stdin-config=false (default is $ARVADOS_CONFIG)")
sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
+ brokenNodeHook := flags.String("broken-node-hook", "", "script to run if node is detected to be broken (for example, Docker daemon is not running)")
flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
ignoreDetachFlag := false
ignoreDetachFlag = true
}
- if err := flags.Parse(args); err == flag.ErrHelp {
- return 0
- } else if err != nil {
- log.Print(err)
- return 1
+ if ok, code := cmd.ParseFlags(flags, prog, args, "container-uuid", stderr); !ok {
+ return code
+ } else if !*list && flags.NArg() != 1 {
+ fmt.Fprintf(stderr, "missing required argument: container-uuid (try -help)\n")
+ return 2
}
containerUUID := flags.Arg(0)
return 1
}
+ var keepstoreLogbuf bufThenWrite
var conf ConfigData
if *stdinConfig {
err := json.NewDecoder(stdin).Decode(&conf)
// fill it using the container UUID prefix.
conf.Cluster.ClusterID = containerUUID[:5]
}
+ } else {
+ conf = hpcConfData(containerUUID, *configFile, io.MultiWriter(&keepstoreLogbuf, stderr))
}
log.Printf("crunch-run %s started", cmd.Version.String())
arvadosclient.CertFiles = []string{*caCertsPath}
}
- var keepstoreLogbuf bufThenWrite
keepstore, err := startLocalKeepstore(conf, io.MultiWriter(&keepstoreLogbuf, stderr))
if err != nil {
log.Print(err)
}
defer cr.executor.Close()
+ cr.brokenNodeHook = *brokenNodeHook
+
gwAuthSecret := os.Getenv("GatewayAuthSecret")
os.Unsetenv("GatewayAuthSecret")
if gwAuthSecret == "" {
// dispatcher did not tell us which external IP
// address to advertise --> no gateway service
cr.CrunchLog.Printf("Not starting a gateway server (GatewayAddress was not provided by dispatcher)")
- } else if de, ok := cr.executor.(*dockerExecutor); ok {
+ } else {
cr.gateway = Gateway{
- Address: gwListen,
- AuthSecret: gwAuthSecret,
- ContainerUUID: containerUUID,
- DockerContainerID: &de.containerID,
- Log: cr.CrunchLog,
- ContainerIPAddress: dockerContainerIPAddress(&de.containerID),
+ Address: gwListen,
+ AuthSecret: gwAuthSecret,
+ ContainerUUID: containerUUID,
+ Target: cr.executor,
+ Log: cr.CrunchLog,
}
err = cr.gateway.Start()
if err != nil {
cr.enableNetwork = *enableNetwork
cr.networkMode = *networkMode
if *cgroupParentSubsystem != "" {
- p := findCgroup(*cgroupParentSubsystem)
+ p, err := findCgroup(*cgroupParentSubsystem)
+ if err != nil {
+ log.Printf("fatal: cgroup parent subsystem: %s", err)
+ return 1
+ }
cr.setCgroupParent = p
cr.expectCgroupParent = p
}
return 0
}
+// Try to load ConfigData in hpc (slurm/lsf) environment. This means
+// loading the cluster config from the specified file and (if that
+// works) getting the runtime_constraints container field from
+// controller to determine # VCPUs so we can calculate KeepBuffers.
+func hpcConfData(uuid string, configFile string, stderr io.Writer) ConfigData {
+ var conf ConfigData
+ conf.Cluster = loadClusterConfigFile(configFile, stderr)
+ if conf.Cluster == nil {
+ // skip loading the container record -- we won't be
+ // able to start local keepstore anyway.
+ return conf
+ }
+ arv, err := arvadosclient.MakeArvadosClient()
+ if err != nil {
+ fmt.Fprintf(stderr, "error setting up arvadosclient: %s\n", err)
+ return conf
+ }
+ arv.Retries = 8
+ var ctr arvados.Container
+ err = arv.Call("GET", "containers", uuid, "", arvadosclient.Dict{"select": []string{"runtime_constraints"}}, &ctr)
+ if err != nil {
+ fmt.Fprintf(stderr, "error getting container record: %s\n", err)
+ return conf
+ }
+ if ctr.RuntimeConstraints.VCPUs > 0 {
+ conf.KeepBuffers = ctr.RuntimeConstraints.VCPUs * conf.Cluster.Containers.LocalKeepBlobBuffersPerVCPU
+ }
+ return conf
+}
+
+// Load cluster config file from given path. If an error occurs, log
+// the error to stderr and return nil.
+func loadClusterConfigFile(path string, stderr io.Writer) *arvados.Cluster {
+ ldr := config.NewLoader(&bytes.Buffer{}, ctxlog.New(stderr, "plain", "info"))
+ ldr.Path = path
+ cfg, err := ldr.Load()
+ if err != nil {
+ fmt.Fprintf(stderr, "could not load config file %s: %s\n", path, err)
+ return nil
+ }
+ cluster, err := cfg.GetCluster("")
+ if err != nil {
+ fmt.Fprintf(stderr, "could not use config file %s: %s\n", path, err)
+ return nil
+ }
+ fmt.Fprintf(stderr, "loaded config file %s\n", path)
+ return cluster
+}
+
func startLocalKeepstore(configData ConfigData, logbuf io.Writer) (*exec.Cmd, error) {
- if configData.Cluster == nil || configData.KeepBuffers < 1 {
+ if configData.KeepBuffers < 1 {
+ fmt.Fprintf(logbuf, "not starting a local keepstore process because KeepBuffers=%v in config\n", configData.KeepBuffers)
+ return nil, nil
+ }
+ if configData.Cluster == nil {
+ fmt.Fprint(logbuf, "not starting a local keepstore process because cluster config file was not loaded\n")
return nil, nil
}
for uuid, vol := range configData.Cluster.Volumes {
os.Setenv("ARVADOS_KEEP_SERVICES", url)
return cmd, nil
}
+
+// return current uid, gid, groups in a format suitable for logging:
+// "crunch-run process has uid=1234(arvados) gid=1234(arvados)
+// groups=1234(arvados),114(fuse)"
+func currentUserAndGroups() string {
+ u, err := user.Current()
+ if err != nil {
+ return fmt.Sprintf("error getting current user ID: %s", err)
+ }
+ s := fmt.Sprintf("crunch-run process has uid=%s(%s) gid=%s", u.Uid, u.Username, u.Gid)
+ if g, err := user.LookupGroupId(u.Gid); err == nil {
+ s += fmt.Sprintf("(%s)", g.Name)
+ }
+ s += " groups="
+ if gids, err := u.GroupIds(); err == nil {
+ for i, gid := range gids {
+ if i > 0 {
+ s += ","
+ }
+ s += gid
+ if g, err := user.LookupGroupId(gid); err == nil {
+ s += fmt.Sprintf("(%s)", g.Name)
+ }
+ }
+ }
+ return s
+}
projects / arvados.git / blobdiff