X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/623ffe7320d0a159ba9a5912fc1948cac12ad505..469ea187586ea8017e26874c2d80414ce7571fae:/lib/crunchrun/crunchrun.go diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go index 8f3a302039..30871e7349 100644 --- a/lib/crunchrun/crunchrun.go +++ b/lib/crunchrun/crunchrun.go @@ -19,6 +19,7 @@ import ( "os" "os/exec" "os/signal" + "os/user" "path" "path/filepath" "regexp" @@ -31,11 +32,14 @@ import ( "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{} @@ -165,6 +169,7 @@ type ContainerRunner 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 @@ -208,10 +213,9 @@ var errorBlacklist = []string{ "(?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) @@ -221,9 +225,9 @@ func (runner *ContainerRunner) runBrokenNodeHook() { } 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() @@ -418,7 +422,7 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) { "--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") } @@ -452,8 +456,8 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) { 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" { @@ -522,8 +526,7 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) { } } 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 { @@ -583,9 +586,32 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) { 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} } @@ -617,10 +643,15 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) { } 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) @@ -981,20 +1012,26 @@ func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[st 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, }) } @@ -1045,6 +1082,20 @@ func (runner *ContainerRunner) WaitFinish() error { } 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) @@ -1427,7 +1478,11 @@ func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, 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 { @@ -1672,6 +1727,7 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s 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") @@ -1680,6 +1736,7 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s 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 @@ -1694,11 +1751,11 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s 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) @@ -1717,6 +1774,7 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s return 1 } + var keepstoreLogbuf bufThenWrite var conf ConfigData if *stdinConfig { err := json.NewDecoder(stdin).Decode(&conf) @@ -1738,6 +1796,8 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s // 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()) @@ -1747,7 +1807,6 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s arvadosclient.CertFiles = []string{*caCertsPath} } - var keepstoreLogbuf bufThenWrite keepstore, err := startLocalKeepstore(conf, io.MultiWriter(&keepstoreLogbuf, stderr)) if err != nil { log.Print(err) @@ -1833,6 +1892,8 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s } defer cr.executor.Close() + cr.brokenNodeHook = *brokenNodeHook + gwAuthSecret := os.Getenv("GatewayAuthSecret") os.Unsetenv("GatewayAuthSecret") if gwAuthSecret == "" { @@ -1843,14 +1904,13 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s // 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 { @@ -1873,7 +1933,11 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s 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 } @@ -1902,8 +1966,62 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s 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 { @@ -1997,3 +2115,30 @@ func startLocalKeepstore(configData ConfigData, logbuf io.Writer) (*exec.Cmd, er 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 +}