services/datamanager/collection/collection.go

   1 // Deals with parsing Collection responses from API Server.
   2
   3 package collection
   4
   5 import (
   6         "flag"
   7         "fmt"
   8         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
   9         "git.curoverse.com/arvados.git/sdk/go/blockdigest"
  10         "git.curoverse.com/arvados.git/sdk/go/logger"
  11         "git.curoverse.com/arvados.git/sdk/go/manifest"
  12         "git.curoverse.com/arvados.git/sdk/go/util"
  13         "log"
  14         "os"
  15         "runtime/pprof"
  16         "time"
  17 )
  18
  19 var (
  20         HeapProfileFilename string
  21         // globals for debugging
  22         totalManifestSize uint64
  23         maxManifestSize   uint64
  24 )
  25
  26 // Collection representation
  27 type Collection struct {
  28         UUID              string
  29         OwnerUUID         string
  30         ReplicationLevel  int
  31         BlockDigestToSize map[blockdigest.BlockDigest]int
  32         TotalSize         int
  33 }
  34
  35 // ReadCollections holds information about collections from API server
  36 type ReadCollections struct {
  37         ReadAllCollections        bool
  38         UUIDToCollection          map[string]Collection
  39         OwnerToCollectionSize     map[string]int
  40         BlockToDesiredReplication map[blockdigest.DigestWithSize]int
  41         CollectionUUIDToIndex     map[string]int
  42         CollectionIndexToUUID     []string
  43         BlockToCollectionIndices  map[blockdigest.DigestWithSize][]int
  44         Err                       error
  45 }
  46
  47 // GetCollectionsParams params
  48 type GetCollectionsParams struct {
  49         Client    arvadosclient.ArvadosClient
  50         Logger    *logger.Logger
  51         BatchSize int
  52 }
  53
  54 // SdkCollectionInfo holds collection info from api
  55 type SdkCollectionInfo struct {
  56         UUID         string    `json:"uuid"`
  57         OwnerUUID    string    `json:"owner_uuid"`
  58         Redundancy   int       `json:"redundancy"`
  59         ModifiedAt   time.Time `json:"modified_at"`
  60         ManifestText string    `json:"manifest_text"`
  61 }
  62
  63 // SdkCollectionList lists collections from api
  64 type SdkCollectionList struct {
  65         ItemsAvailable int                 `json:"items_available"`
  66         Items          []SdkCollectionInfo `json:"items"`
  67 }
  68
  69 func init() {
  70         flag.StringVar(&HeapProfileFilename,
  71                 "heap-profile",
  72                 "",
  73                 "File to write the heap profiles to. Leave blank to skip profiling.")
  74 }
  75
  76 // WriteHeapProfile writes the heap profile to a file for later review.
  77 // Since a file is expected to only contain a single heap profile this
  78 // function overwrites the previously written profile, so it is safe
  79 // to call multiple times in a single run.
  80 // Otherwise we would see cumulative numbers as explained here:
  81 // https://groups.google.com/d/msg/golang-nuts/ZyHciRglQYc/2nh4Ndu2fZcJ
  82 func WriteHeapProfile() error {
  83         if HeapProfileFilename != "" {
  84                 heapProfile, err := os.Create(HeapProfileFilename)
  85                 if err != nil {
  86                         return err
  87                 }
  88
  89                 defer heapProfile.Close()
  90
  91                 err = pprof.WriteHeapProfile(heapProfile)
  92                 return err
  93         }
  94
  95         return nil
  96 }
  97
  98 // GetCollectionsAndSummarize gets collections from api and summarizes
  99 func GetCollectionsAndSummarize(arvLogger *logger.Logger, params GetCollectionsParams) (results ReadCollections) {
 100         results, err := GetCollections(params)
 101         if err != nil {
 102                 results.Err = err
 103                 return
 104         }
 105
 106         results.Summarize(params.Logger)
 107
 108         log.Printf("Uuid to Size used: %v", results.OwnerToCollectionSize)
 109         log.Printf("Read and processed %d collections",
 110                 len(results.UUIDToCollection))
 111
 112         // TODO(misha): Add a "readonly" flag. If we're in readonly mode,
 113         // lots of behaviors can become warnings (and obviously we can't
 114         // write anything).
 115         // if !readCollections.ReadAllCollections {
 116         //      log.Fatalf("Did not read all collections")
 117         // }
 118
 119         return
 120 }
 121
 122 // GetCollections gets collections from api
 123 func GetCollections(params GetCollectionsParams) (results ReadCollections, err error) {
 124         if &params.Client == nil {
 125                 err = fmt.Errorf("params.Client passed to GetCollections() should " +
 126                         "contain a valid ArvadosClient, but instead it is nil.")
 127                 return
 128         }
 129
 130         fieldsWanted := []string{"manifest_text",
 131                 "owner_uuid",
 132                 "uuid",
 133                 "redundancy",
 134                 "modified_at"}
 135
 136         sdkParams := arvadosclient.Dict{
 137                 "select":  fieldsWanted,
 138                 "order":   []string{"modified_at ASC"},
 139                 "filters": [][]string{[]string{"modified_at", ">=", "1900-01-01T00:00:00Z"}}}
 140
 141         if params.BatchSize > 0 {
 142                 sdkParams["limit"] = params.BatchSize
 143         }
 144
 145         var defaultReplicationLevel int
 146         {
 147                 var value interface{}
 148                 value, err = params.Client.Discovery("defaultCollectionReplication")
 149                 if err != nil {
 150                         return
 151                 }
 152
 153                 defaultReplicationLevel = int(value.(float64))
 154                 if defaultReplicationLevel <= 0 {
 155                         err = fmt.Errorf("Default collection replication returned by arvados SDK "+
 156                                 "should be a positive integer but instead it was %d.",
 157                                 defaultReplicationLevel)
 158                         return
 159                 }
 160         }
 161
 162         initialNumberOfCollectionsAvailable, err :=
 163                 util.NumberItemsAvailable(params.Client, "collections")
 164         if err != nil {
 165                 return
 166         }
 167         // Include a 1% margin for collections added while we're reading so
 168         // that we don't have to grow the map in most cases.
 169         maxExpectedCollections := int(
 170                 float64(initialNumberOfCollectionsAvailable) * 1.01)
 171         results.UUIDToCollection = make(map[string]Collection, maxExpectedCollections)
 172
 173         if params.Logger != nil {
 174                 params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
 175                         collectionInfo := logger.GetOrCreateMap(p, "collection_info")
 176                         collectionInfo["num_collections_at_start"] = initialNumberOfCollectionsAvailable
 177                         collectionInfo["batch_size"] = params.BatchSize
 178                         collectionInfo["default_replication_level"] = defaultReplicationLevel
 179                 })
 180         }
 181
 182         // These values are just for getting the loop to run the first time,
 183         // afterwards they'll be set to real values.
 184         previousTotalCollections := -1
 185         totalCollections := 0
 186         for totalCollections > previousTotalCollections {
 187                 // We're still finding new collections
 188
 189                 // Write the heap profile for examining memory usage
 190                 err = WriteHeapProfile()
 191                 if err != nil {
 192                         return
 193                 }
 194
 195                 // Get next batch of collections.
 196                 var collections SdkCollectionList
 197                 err = params.Client.List("collections", sdkParams, &collections)
 198                 if err != nil {
 199                         return
 200                 }
 201
 202                 // Process collection and update our date filter.
 203                 var latestModificationDate time.Time
 204                 latestModificationDate, err = ProcessCollections(params.Logger,
 205                         collections.Items,
 206                         defaultReplicationLevel,
 207                         results.UUIDToCollection)
 208                 if err != nil {
 209                         return
 210                 }
 211                 sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339)
 212
 213                 // update counts
 214                 previousTotalCollections = totalCollections
 215                 totalCollections = len(results.UUIDToCollection)
 216
 217                 log.Printf("%d collections read, %d new in last batch, "+
 218                         "%s latest modified date, %.0f %d %d avg,max,total manifest size",
 219                         totalCollections,
 220                         totalCollections-previousTotalCollections,
 221                         sdkParams["filters"].([][]string)[0][2],
 222                         float32(totalManifestSize)/float32(totalCollections),
 223                         maxManifestSize, totalManifestSize)
 224
 225                 if params.Logger != nil {
 226                         params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
 227                                 collectionInfo := logger.GetOrCreateMap(p, "collection_info")
 228                                 collectionInfo["collections_read"] = totalCollections
 229                                 collectionInfo["latest_modified_date_seen"] = sdkParams["filters"].([][]string)[0][2]
 230                                 collectionInfo["total_manifest_size"] = totalManifestSize
 231                                 collectionInfo["max_manifest_size"] = maxManifestSize
 232                         })
 233                 }
 234         }
 235
 236         // Write the heap profile for examining memory usage
 237         err = WriteHeapProfile()
 238
 239         return
 240 }
 241
 242 // StrCopy returns a newly allocated string.
 243 // It is useful to copy slices so that the garbage collector can reuse
 244 // the memory of the longer strings they came from.
 245 func StrCopy(s string) string {
 246         return string([]byte(s))
 247 }
 248
 249 // ProcessCollections read from api server
 250 func ProcessCollections(arvLogger *logger.Logger,
 251         receivedCollections []SdkCollectionInfo,
 252         defaultReplicationLevel int,
 253         UUIDToCollection map[string]Collection) (latestModificationDate time.Time, err error) {
 254         for _, sdkCollection := range receivedCollections {
 255                 collection := Collection{UUID: StrCopy(sdkCollection.UUID),
 256                         OwnerUUID:         StrCopy(sdkCollection.OwnerUUID),
 257                         ReplicationLevel:  sdkCollection.Redundancy,
 258                         BlockDigestToSize: make(map[blockdigest.BlockDigest]int)}
 259
 260                 if sdkCollection.ModifiedAt.IsZero() {
 261                         return latestModificationDate, fmt.Errorf(
 262                                 "Arvados SDK collection returned with unexpected zero "+
 263                                         "modification date. This probably means that either we failed to "+
 264                                         "parse the modification date or the API server has changed how "+
 265                                         "it returns modification dates: %+v",
 266                                 collection)
 267                 }
 268
 269                 if sdkCollection.ModifiedAt.After(latestModificationDate) {
 270                         latestModificationDate = sdkCollection.ModifiedAt
 271                 }
 272
 273                 if collection.ReplicationLevel == 0 {
 274                         collection.ReplicationLevel = defaultReplicationLevel
 275                 }
 276
 277                 manifest := manifest.Manifest{sdkCollection.ManifestText}
 278                 manifestSize := uint64(len(sdkCollection.ManifestText))
 279
 280                 if _, alreadySeen := UUIDToCollection[collection.UUID]; !alreadySeen {
 281                         totalManifestSize += manifestSize
 282                 }
 283                 if manifestSize > maxManifestSize {
 284                         maxManifestSize = manifestSize
 285                 }
 286
 287                 blockChannel := manifest.BlockIterWithDuplicates()
 288                 for block := range blockChannel {
 289                         if storedSize, stored := collection.BlockDigestToSize[block.Digest]; stored && storedSize != block.Size {
 290                                 err = fmt.Errorf(
 291                                         "Collection %s contains multiple sizes (%d and %d) for block %s",
 292                                         collection.UUID,
 293                                         storedSize,
 294                                         block.Size,
 295                                         block.Digest)
 296                                 return
 297                         }
 298                         collection.BlockDigestToSize[block.Digest] = block.Size
 299                 }
 300                 collection.TotalSize = 0
 301                 for _, size := range collection.BlockDigestToSize {
 302                         collection.TotalSize += size
 303                 }
 304                 UUIDToCollection[collection.UUID] = collection
 305
 306                 // Clear out all the manifest strings that we don't need anymore.
 307                 // These hopefully form the bulk of our memory usage.
 308                 manifest.Text = ""
 309                 sdkCollection.ManifestText = ""
 310         }
 311
 312         return
 313 }
 314
 315 // Summarize the collections read
 316 func (readCollections *ReadCollections) Summarize(arvLogger *logger.Logger) {
 317         readCollections.OwnerToCollectionSize = make(map[string]int)
 318         readCollections.BlockToDesiredReplication = make(map[blockdigest.DigestWithSize]int)
 319         numCollections := len(readCollections.UUIDToCollection)
 320         readCollections.CollectionUUIDToIndex = make(map[string]int, numCollections)
 321         readCollections.CollectionIndexToUUID = make([]string, 0, numCollections)
 322         readCollections.BlockToCollectionIndices = make(map[blockdigest.DigestWithSize][]int)
 323
 324         for _, coll := range readCollections.UUIDToCollection {
 325                 collectionIndex := len(readCollections.CollectionIndexToUUID)
 326                 readCollections.CollectionIndexToUUID =
 327                         append(readCollections.CollectionIndexToUUID, coll.UUID)
 328                 readCollections.CollectionUUIDToIndex[coll.UUID] = collectionIndex
 329
 330                 readCollections.OwnerToCollectionSize[coll.OwnerUUID] =
 331                         readCollections.OwnerToCollectionSize[coll.OwnerUUID] + coll.TotalSize
 332
 333                 for block, size := range coll.BlockDigestToSize {
 334                         locator := blockdigest.DigestWithSize{Digest: block, Size: uint32(size)}
 335                         readCollections.BlockToCollectionIndices[locator] =
 336                                 append(readCollections.BlockToCollectionIndices[locator],
 337                                         collectionIndex)
 338                         storedReplication := readCollections.BlockToDesiredReplication[locator]
 339                         if coll.ReplicationLevel > storedReplication {
 340                                 readCollections.BlockToDesiredReplication[locator] =
 341                                         coll.ReplicationLevel
 342                         }
 343                 }
 344         }
 345
 346         if arvLogger != nil {
 347                 arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
 348                         collectionInfo := logger.GetOrCreateMap(p, "collection_info")
 349                         // Since maps are shallow copied, we run a risk of concurrent
 350                         // updates here. By copying results.OwnerToCollectionSize into
 351                         // the log, we're assuming that it won't be updated.
 352                         collectionInfo["owner_to_collection_size"] =
 353                                 readCollections.OwnerToCollectionSize
 354                         collectionInfo["distinct_blocks_named"] =
 355                                 len(readCollections.BlockToDesiredReplication)
 356                 })
 357         }
 358
 359         return
 360 }