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