arvados.go

   1 package main
   2
   3 import (
   4         "encoding/json"
   5         "errors"
   6         "fmt"
   7         "io/ioutil"
   8         "net/url"
   9         "os"
  10         "regexp"
  11         "strings"
  12         "sync"
  13         "time"
  14
  15         "git.arvados.org/arvados.git/sdk/go/arvados"
  16         "git.arvados.org/arvados.git/sdk/go/arvadosclient"
  17         "git.arvados.org/arvados.git/sdk/go/keepclient"
  18         log "github.com/sirupsen/logrus"
  19         "golang.org/x/crypto/blake2b"
  20         "golang.org/x/net/websocket"
  21 )
  22
  23 type eventMessage struct {
  24         Status     int
  25         ObjectUUID string `json:"object_uuid"`
  26         EventType  string `json:"event_type"`
  27         Properties struct {
  28                 Text string
  29         }
  30 }
  31
  32 type arvadosClient struct {
  33         *arvados.Client
  34         notifying map[string]map[chan<- eventMessage]int
  35         wantClose chan struct{}
  36         wsconn    *websocket.Conn
  37         mtx       sync.Mutex
  38 }
  39
  40 // Listen for events concerning the given uuids. When an event occurs
  41 // (and after connecting/reconnecting to the event stream), send each
  42 // uuid to ch. If a {ch, uuid} pair is subscribed twice, the uuid will
  43 // be sent only once for each update, but two Unsubscribe calls will
  44 // be needed to stop sending them.
  45 func (client *arvadosClient) Subscribe(ch chan<- eventMessage, uuid string) {
  46         client.mtx.Lock()
  47         defer client.mtx.Unlock()
  48         if client.notifying == nil {
  49                 client.notifying = map[string]map[chan<- eventMessage]int{}
  50                 client.wantClose = make(chan struct{})
  51                 go client.runNotifier()
  52         }
  53         chmap := client.notifying[uuid]
  54         if chmap == nil {
  55                 chmap = map[chan<- eventMessage]int{}
  56                 client.notifying[uuid] = chmap
  57         }
  58         needSub := true
  59         for _, nch := range chmap {
  60                 if nch > 0 {
  61                         needSub = false
  62                         break
  63                 }
  64         }
  65         chmap[ch]++
  66         if needSub && client.wsconn != nil {
  67                 go json.NewEncoder(client.wsconn).Encode(map[string]interface{}{
  68                         "method": "subscribe",
  69                         "filters": [][]interface{}{
  70                                 {"object_uuid", "=", uuid},
  71                                 {"event_type", "in", []string{"stderr", "crunch-run", "update"}},
  72                         },
  73                 })
  74         }
  75 }
  76
  77 func (client *arvadosClient) Unsubscribe(ch chan<- eventMessage, uuid string) {
  78         client.mtx.Lock()
  79         defer client.mtx.Unlock()
  80         chmap := client.notifying[uuid]
  81         if n := chmap[ch] - 1; n == 0 {
  82                 delete(chmap, ch)
  83                 if len(chmap) == 0 {
  84                         delete(client.notifying, uuid)
  85                 }
  86                 if client.wsconn != nil {
  87                         go json.NewEncoder(client.wsconn).Encode(map[string]interface{}{
  88                                 "method": "unsubscribe",
  89                                 "filters": [][]interface{}{
  90                                         {"object_uuid", "=", uuid},
  91                                         {"event_type", "in", []string{"stderr", "crunch-run", "update"}},
  92                                 },
  93                         })
  94                 }
  95         } else if n > 0 {
  96                 chmap[ch] = n
  97         }
  98 }
  99
 100 func (client *arvadosClient) Close() {
 101         client.mtx.Lock()
 102         defer client.mtx.Unlock()
 103         if client.notifying != nil {
 104                 client.notifying = nil
 105                 close(client.wantClose)
 106         }
 107 }
 108
 109 func (client *arvadosClient) runNotifier() {
 110 reconnect:
 111         for {
 112                 var cluster arvados.Cluster
 113                 err := client.RequestAndDecode(&cluster, "GET", arvados.EndpointConfigGet.Path, nil, nil)
 114                 if err != nil {
 115                         log.Warnf("error getting cluster config: %s", err)
 116                         time.Sleep(5 * time.Second)
 117                         continue reconnect
 118                 }
 119                 wsURL := cluster.Services.Websocket.ExternalURL
 120                 wsURL.Scheme = strings.Replace(wsURL.Scheme, "http", "ws", 1)
 121                 wsURL.Path = "/websocket"
 122                 wsURLNoToken := wsURL.String()
 123                 wsURL.RawQuery = url.Values{"api_token": []string{client.AuthToken}}.Encode()
 124                 conn, err := websocket.Dial(wsURL.String(), "", cluster.Services.Controller.ExternalURL.String())
 125                 if err != nil {
 126                         log.Warnf("websocket connection error: %s", err)
 127                         time.Sleep(5 * time.Second)
 128                         continue reconnect
 129                 }
 130                 log.Printf("connected to websocket at %s", wsURLNoToken)
 131
 132                 client.mtx.Lock()
 133                 client.wsconn = conn
 134                 resubscribe := make([]string, 0, len(client.notifying))
 135                 for uuid := range client.notifying {
 136                         resubscribe = append(resubscribe, uuid)
 137                 }
 138                 client.mtx.Unlock()
 139
 140                 go func() {
 141                         w := json.NewEncoder(conn)
 142                         for _, uuid := range resubscribe {
 143                                 w.Encode(map[string]interface{}{
 144                                         "method": "subscribe",
 145                                         "filters": [][]interface{}{
 146                                                 {"object_uuid", "=", uuid},
 147                                                 {"event_type", "in", []string{"stderr", "crunch-run", "update"}},
 148                                         },
 149                                 })
 150                         }
 151                 }()
 152
 153                 r := json.NewDecoder(conn)
 154                 for {
 155                         var msg eventMessage
 156                         err := r.Decode(&msg)
 157                         select {
 158                         case <-client.wantClose:
 159                                 return
 160                         default:
 161                                 if err != nil {
 162                                         log.Printf("error decoding websocket message: %s", err)
 163                                         client.mtx.Lock()
 164                                         client.wsconn = nil
 165                                         client.mtx.Unlock()
 166                                         go conn.Close()
 167                                         continue reconnect
 168                                 }
 169                                 client.mtx.Lock()
 170                                 for ch := range client.notifying[msg.ObjectUUID] {
 171                                         ch <- msg
 172                                 }
 173                                 client.mtx.Unlock()
 174                         }
 175                 }
 176         }
 177 }
 178
 179 type arvadosContainerRunner struct {
 180         Client      *arvados.Client
 181         Name        string
 182         ProjectUUID string
 183         VCPUs       int
 184         RAM         int64
 185         Prog        string // if empty, run /proc/self/exe
 186         Args        []string
 187         Mounts      map[string]map[string]interface{}
 188         Priority    int
 189 }
 190
 191 func (runner *arvadosContainerRunner) Run() (string, error) {
 192         if runner.ProjectUUID == "" {
 193                 return "", errors.New("cannot run arvados container: ProjectUUID not provided")
 194         }
 195
 196         mounts := map[string]map[string]interface{}{
 197                 "/mnt/output": {
 198                         "kind":     "collection",
 199                         "writable": true,
 200                 },
 201         }
 202         for path, mnt := range runner.Mounts {
 203                 mounts[path] = mnt
 204         }
 205
 206         prog := runner.Prog
 207         if prog == "" {
 208                 prog = "/mnt/cmd/lightning"
 209                 cmdUUID, err := runner.makeCommandCollection()
 210                 if err != nil {
 211                         return "", err
 212                 }
 213                 mounts["/mnt/cmd"] = map[string]interface{}{
 214                         "kind": "collection",
 215                         "uuid": cmdUUID,
 216                 }
 217         }
 218         command := append([]string{prog}, runner.Args...)
 219
 220         priority := runner.Priority
 221         if priority < 1 {
 222                 priority = 500
 223         }
 224         rc := arvados.RuntimeConstraints{
 225                 VCPUs:        runner.VCPUs,
 226                 RAM:          runner.RAM,
 227                 KeepCacheRAM: (1 << 26) * 2 * int64(runner.VCPUs),
 228         }
 229         var cr arvados.ContainerRequest
 230         err := runner.Client.RequestAndDecode(&cr, "POST", "arvados/v1/container_requests", nil, map[string]interface{}{
 231                 "container_request": map[string]interface{}{
 232                         "owner_uuid":          runner.ProjectUUID,
 233                         "name":                runner.Name,
 234                         "container_image":     "lightning-runtime",
 235                         "command":             command,
 236                         "mounts":              mounts,
 237                         "use_existing":        true,
 238                         "output_path":         "/mnt/output",
 239                         "runtime_constraints": rc,
 240                         "priority":            runner.Priority,
 241                         "state":               arvados.ContainerRequestStateCommitted,
 242                 },
 243         })
 244         if err != nil {
 245                 return "", err
 246         }
 247         log.Printf("container request UUID: %s", cr.UUID)
 248         log.Printf("container UUID: %s", cr.ContainerUUID)
 249
 250         logch := make(chan eventMessage)
 251         client := arvadosClient{Client: runner.Client}
 252         defer client.Close()
 253         subscribedUUID := ""
 254         defer func() {
 255                 if subscribedUUID != "" {
 256                         client.Unsubscribe(logch, subscribedUUID)
 257                 }
 258         }()
 259
 260         ticker := time.NewTicker(5 * time.Second)
 261         defer ticker.Stop()
 262
 263         lastState := cr.State
 264         refreshCR := func() {
 265                 err = runner.Client.RequestAndDecode(&cr, "GET", "arvados/v1/container_requests/"+cr.UUID, nil, nil)
 266                 if err != nil {
 267                         log.Printf("error getting container request: %s", err)
 268                         return
 269                 }
 270                 if lastState != cr.State {
 271                         log.Printf("container request state: %s", cr.State)
 272                         lastState = cr.State
 273                 }
 274                 if subscribedUUID != cr.ContainerUUID {
 275                         if subscribedUUID != "" {
 276                                 client.Unsubscribe(logch, subscribedUUID)
 277                         }
 278                         client.Subscribe(logch, cr.ContainerUUID)
 279                         subscribedUUID = cr.ContainerUUID
 280                 }
 281         }
 282
 283         for cr.State != arvados.ContainerRequestStateFinal {
 284                 select {
 285                 case <-ticker.C:
 286                         refreshCR()
 287                 case msg := <-logch:
 288                         switch msg.EventType {
 289                         case "update":
 290                                 refreshCR()
 291                         default:
 292                                 for _, line := range strings.Split(msg.Properties.Text, "\n") {
 293                                         if line != "" {
 294                                                 log.Print(line)
 295                                         }
 296                                 }
 297                         }
 298                 }
 299         }
 300
 301         var c arvados.Container
 302         err = runner.Client.RequestAndDecode(&c, "GET", "arvados/v1/containers/"+cr.ContainerUUID, nil, nil)
 303         if err != nil {
 304                 return "", err
 305         } else if c.State != arvados.ContainerStateComplete {
 306                 return "", fmt.Errorf("container did not complete: %s", c.State)
 307         } else if c.ExitCode != 0 {
 308                 return "", fmt.Errorf("container exited %d", c.ExitCode)
 309         }
 310         return cr.OutputUUID, err
 311 }
 312
 313 var collectionInPathRe = regexp.MustCompile(`^(.*/)?([0-9a-f]{32}\+[0-9]+|[0-9a-z]{5}-[0-9a-z]{5}-[0-9a-z]{15})(/.*)?$`)
 314
 315 func (runner *arvadosContainerRunner) TranslatePaths(paths ...*string) error {
 316         if runner.Mounts == nil {
 317                 runner.Mounts = make(map[string]map[string]interface{})
 318         }
 319         for _, path := range paths {
 320                 if *path == "" || *path == "-" {
 321                         continue
 322                 }
 323                 m := collectionInPathRe.FindStringSubmatch(*path)
 324                 if m == nil {
 325                         return fmt.Errorf("cannot find uuid in path: %q", *path)
 326                 }
 327                 uuid := m[2]
 328                 mnt, ok := runner.Mounts["/mnt/"+uuid]
 329                 if !ok {
 330                         mnt = map[string]interface{}{
 331                                 "kind": "collection",
 332                                 "uuid": uuid,
 333                         }
 334                         runner.Mounts["/mnt/"+uuid] = mnt
 335                 }
 336                 *path = "/mnt/" + uuid + m[3]
 337         }
 338         return nil
 339 }
 340
 341 func (runner *arvadosContainerRunner) makeCommandCollection() (string, error) {
 342         exe, err := ioutil.ReadFile("/proc/self/exe")
 343         if err != nil {
 344                 return "", err
 345         }
 346         b2 := blake2b.Sum256(exe)
 347         cname := fmt.Sprintf("lightning-%x", b2)
 348         var existing arvados.CollectionList
 349         err = runner.Client.RequestAndDecode(&existing, "GET", "arvados/v1/collections", nil, arvados.ListOptions{
 350                 Limit: 1,
 351                 Count: "none",
 352                 Filters: []arvados.Filter{
 353                         {Attr: "name", Operator: "=", Operand: cname},
 354                         {Attr: "owner_uuid", Operator: "=", Operand: runner.ProjectUUID},
 355                 },
 356         })
 357         if err != nil {
 358                 return "", err
 359         }
 360         if len(existing.Items) > 0 {
 361                 uuid := existing.Items[0].UUID
 362                 log.Printf("using lightning binary in existing collection %s (name is %q; did not verify whether content matches)", uuid, cname)
 363                 return uuid, nil
 364         }
 365         log.Printf("writing lightning binary to new collection %q", cname)
 366         ac, err := arvadosclient.New(runner.Client)
 367         if err != nil {
 368                 return "", err
 369         }
 370         kc := keepclient.New(ac)
 371         var coll arvados.Collection
 372         fs, err := coll.FileSystem(runner.Client, kc)
 373         if err != nil {
 374                 return "", err
 375         }
 376         f, err := fs.OpenFile("lightning", os.O_CREATE|os.O_WRONLY, 0777)
 377         if err != nil {
 378                 return "", err
 379         }
 380         _, err = f.Write(exe)
 381         if err != nil {
 382                 return "", err
 383         }
 384         err = f.Close()
 385         if err != nil {
 386                 return "", err
 387         }
 388         mtxt, err := fs.MarshalManifest(".")
 389         if err != nil {
 390                 return "", err
 391         }
 392         err = runner.Client.RequestAndDecode(&coll, "POST", "arvados/v1/collections", nil, map[string]interface{}{
 393                 "collection": map[string]interface{}{
 394                         "owner_uuid":    runner.ProjectUUID,
 395                         "manifest_text": mtxt,
 396                         "name":          cname,
 397                 },
 398         })
 399         if err != nil {
 400                 return "", err
 401         }
 402         log.Printf("stored lightning binary in new collection %s", coll.UUID)
 403         return coll.UUID, nil
 404 }