X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/043e2d7fa61b4954f0d84c6e4281e37a4f6f865f..cdad40f38151c5d678f13787853f361566fbcd43:/services/datamanager/collection/collection.go diff --git a/services/datamanager/collection/collection.go b/services/datamanager/collection/collection.go index 48db7bdafa..7cc3ff7204 100644 --- a/services/datamanager/collection/collection.go +++ b/services/datamanager/collection/collection.go @@ -1,86 +1,388 @@ -/* Deals with parsing Collection responses from API Server. */ +// Deals with parsing Collection responses from API Server. package collection import ( + "flag" + "fmt" "git.curoverse.com/arvados.git/sdk/go/arvadosclient" - "git.curoverse.com/arvados.git/services/datamanager/manifest" + "git.curoverse.com/arvados.git/sdk/go/blockdigest" + "git.curoverse.com/arvados.git/sdk/go/logger" + "git.curoverse.com/arvados.git/sdk/go/manifest" + "git.curoverse.com/arvados.git/sdk/go/util" "log" + "os" + "runtime/pprof" + "time" ) +var ( + HeapProfileFilename string +) + +// Collection representation type Collection struct { - BlockDigestToSize map[string]int - ReplicationLevel int - Uuid string - OwnerUuid string + UUID string + OwnerUUID string + ReplicationLevel int + BlockDigestToSize map[blockdigest.BlockDigest]int + TotalSize int +} + +// ReadCollections holds information about collections from API server +type ReadCollections struct { + ReadAllCollections bool + UUIDToCollection map[string]Collection + OwnerToCollectionSize map[string]int + BlockToDesiredReplication map[blockdigest.DigestWithSize]int + CollectionUUIDToIndex map[string]int + CollectionIndexToUUID []string + BlockToCollectionIndices map[blockdigest.DigestWithSize][]int +} + +// GetCollectionsParams params +type GetCollectionsParams struct { + Client arvadosclient.ArvadosClient + Logger *logger.Logger + BatchSize int } -type readCollections struct { - ReadAllCollections bool - UuidToCollection map[string]Collection +// SdkCollectionInfo holds collection info from api +type SdkCollectionInfo struct { + UUID string `json:"uuid"` + OwnerUUID string `json:"owner_uuid"` + Redundancy int `json:"redundancy"` + ModifiedAt time.Time `json:"modified_at"` + ManifestText string `json:"manifest_text"` +} + +// SdkCollectionList lists collections from api +type SdkCollectionList struct { + ItemsAvailable int `json:"items_available"` + Items []SdkCollectionInfo `json:"items"` +} + +func init() { + flag.StringVar(&HeapProfileFilename, + "heap-profile", + "", + "File to write the heap profiles to. Leave blank to skip profiling.") +} + +// WriteHeapProfile writes the heap profile to a file for later review. +// Since a file is expected to only contain a single heap profile this +// function overwrites the previously written profile, so it is safe +// to call multiple times in a single run. +// Otherwise we would see cumulative numbers as explained here: +// https://groups.google.com/d/msg/golang-nuts/ZyHciRglQYc/2nh4Ndu2fZcJ +func WriteHeapProfile() error { + if HeapProfileFilename != "" { + heapProfile, err := os.Create(HeapProfileFilename) + if err != nil { + return err + } + + defer heapProfile.Close() + + err = pprof.WriteHeapProfile(heapProfile) + return err + } + + return nil +} + +// GetCollectionsAndSummarize gets collections from api and summarizes +func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections, err error) { + results, err = GetCollections(params) + if err != nil { + return + } + + results.Summarize(params.Logger) + + log.Printf("Uuid to Size used: %v", results.OwnerToCollectionSize) + log.Printf("Read and processed %d collections", + len(results.UUIDToCollection)) + + // TODO(misha): Add a "readonly" flag. If we're in readonly mode, + // lots of behaviors can become warnings (and obviously we can't + // write anything). + // if !readCollections.ReadAllCollections { + // log.Fatalf("Did not read all collections") + // } + + return } -func GetCollections(arv arvadosclient.ArvadosClient) (results readCollections) { +// GetCollections gets collections from api +func GetCollections(params GetCollectionsParams) (results ReadCollections, err error) { + if ¶ms.Client == nil { + err = fmt.Errorf("params.Client passed to GetCollections() should " + + "contain a valid ArvadosClient, but instead it is nil.") + return + } + fieldsWanted := []string{"manifest_text", "owner_uuid", "uuid", - // TODO(misha): Start using the redundancy field. - "redundancy"} + "redundancy", + "modified_at"} + + sdkParams := arvadosclient.Dict{ + "select": fieldsWanted, + "order": []string{"modified_at ASC"}, + "filters": [][]string{[]string{"modified_at", ">=", "1900-01-01T00:00:00Z"}}} - // TODO(misha): Set the limit param with a flag. - params := arvadosclient.Dict{"limit": 1, "select": fieldsWanted} + if params.BatchSize > 0 { + sdkParams["limit"] = params.BatchSize + } + + var defaultReplicationLevel int + { + var value interface{} + value, err = params.Client.Discovery("defaultCollectionReplication") + if err != nil { + return + } - var collections map[string]interface{} - err := arv.List("collections", params, &collections) + defaultReplicationLevel = int(value.(float64)) + if defaultReplicationLevel <= 0 { + err = fmt.Errorf("Default collection replication returned by arvados SDK "+ + "should be a positive integer but instead it was %d.", + defaultReplicationLevel) + return + } + } + + initialNumberOfCollectionsAvailable, err := + util.NumberItemsAvailable(params.Client, "collections") if err != nil { - log.Fatalf("error querying collections: %v", err) + return } + // Include a 1% margin for collections added while we're reading so + // that we don't have to grow the map in most cases. + maxExpectedCollections := int( + float64(initialNumberOfCollectionsAvailable) * 1.01) + results.UUIDToCollection = make(map[string]Collection, maxExpectedCollections) - results.ReadAllCollections = false + if params.Logger != nil { + params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) { + collectionInfo := logger.GetOrCreateMap(p, "collection_info") + collectionInfo["num_collections_at_start"] = initialNumberOfCollectionsAvailable + collectionInfo["batch_size"] = params.BatchSize + collectionInfo["default_replication_level"] = defaultReplicationLevel + }) + } - if value, ok := collections["items"]; ok { - items := value.([]interface{}) + // These values are just for getting the loop to run the first time, + // afterwards they'll be set to real values. + previousTotalCollections := -1 + totalCollections := 0 + for totalCollections > previousTotalCollections { + // We're still finding new collections - { - var itemsAvailable interface{} - if itemsAvailable, ok = collections["items_available"]; !ok { - log.Fatalf("API server did not return the number of items available") - } - numReceived := len(items) - numAvailable := int(itemsAvailable.(float64)) - results.ReadAllCollections = numReceived == numAvailable + // Write the heap profile for examining memory usage + err = WriteHeapProfile() + if err != nil { + return + } + + // Get next batch of collections. + var collections SdkCollectionList + err = params.Client.List("collections", sdkParams, &collections) + if err != nil { + return + } + + // Process collection and update our date filter. + latestModificationDate, maxManifestSize, totalManifestSize, err := ProcessCollections(params.Logger, + collections.Items, + defaultReplicationLevel, + results.UUIDToCollection) + if err != nil { + return results, err + } + sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339) - if (!results.ReadAllCollections) { + // update counts + previousTotalCollections = totalCollections + totalCollections = len(results.UUIDToCollection) + + log.Printf("%d collections read, %d new in last batch, "+ + "%s latest modified date, %.0f %d %d avg,max,total manifest size", + totalCollections, + totalCollections-previousTotalCollections, + sdkParams["filters"].([][]string)[0][2], + float32(totalManifestSize)/float32(totalCollections), + maxManifestSize, totalManifestSize) + + if params.Logger != nil { + params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) { + collectionInfo := logger.GetOrCreateMap(p, "collection_info") + collectionInfo["collections_read"] = totalCollections + collectionInfo["latest_modified_date_seen"] = sdkParams["filters"].([][]string)[0][2] + collectionInfo["total_manifest_size"] = totalManifestSize + collectionInfo["max_manifest_size"] = maxManifestSize + }) + } + } + + // Make one final API request to verify that we have processed all collections available up to the latest modification date + var collections SdkCollectionList + sdkParams["filters"].([][]string)[0][1] = "<=" + sdkParams["limit"] = 0 + err = params.Client.List("collections", sdkParams, &collections) + if err != nil { + return + } + finalNumberOfCollectionsAvailable, err := + util.NumberItemsAvailable(params.Client, "collections") + if err != nil { + return + } + if totalCollections < finalNumberOfCollectionsAvailable { + err = fmt.Errorf("API server indicates a total of %d collections "+ + "available up to %v, but we only retrieved %d. "+ + "Refusing to continue as this could indicate an "+ + "otherwise undetected failure.", + finalNumberOfCollectionsAvailable, + sdkParams["filters"].([][]string)[0][2], + totalCollections) + return + } + + // Write the heap profile for examining memory usage + err = WriteHeapProfile() + + return +} + +// StrCopy returns a newly allocated string. +// It is useful to copy slices so that the garbage collector can reuse +// the memory of the longer strings they came from. +func StrCopy(s string) string { + return string([]byte(s)) +} + +// ProcessCollections read from api server +func ProcessCollections(arvLogger *logger.Logger, + receivedCollections []SdkCollectionInfo, + defaultReplicationLevel int, + UUIDToCollection map[string]Collection, +) ( + latestModificationDate time.Time, + maxManifestSize, totalManifestSize uint64, + err error, +) { + for _, sdkCollection := range receivedCollections { + collection := Collection{UUID: StrCopy(sdkCollection.UUID), + OwnerUUID: StrCopy(sdkCollection.OwnerUUID), + ReplicationLevel: sdkCollection.Redundancy, + BlockDigestToSize: make(map[blockdigest.BlockDigest]int)} + + if sdkCollection.ModifiedAt.IsZero() { + err = fmt.Errorf( + "Arvados SDK collection returned with unexpected zero "+ + "modification date. This probably means that either we failed to "+ + "parse the modification date or the API server has changed how "+ + "it returns modification dates: %+v", + collection) + return + } + + if sdkCollection.ModifiedAt.After(latestModificationDate) { + latestModificationDate = sdkCollection.ModifiedAt + } + + if collection.ReplicationLevel == 0 { + collection.ReplicationLevel = defaultReplicationLevel + } + + manifest := manifest.Manifest{Text: sdkCollection.ManifestText} + manifestSize := uint64(len(sdkCollection.ManifestText)) + + if _, alreadySeen := UUIDToCollection[collection.UUID]; !alreadySeen { + totalManifestSize += manifestSize + } + if manifestSize > maxManifestSize { + maxManifestSize = manifestSize + } + + blockChannel := manifest.BlockIterWithDuplicates() + for block := range blockChannel { + if storedSize, stored := collection.BlockDigestToSize[block.Digest]; stored && storedSize != block.Size { log.Printf( - "ERROR: Did not receive all collections. " + - "Received %d of %d available collections.", - numReceived, - numAvailable) + "Collection %s contains multiple sizes (%d and %d) for block %s", + collection.UUID, + storedSize, + block.Size, + block.Digest) } + collection.BlockDigestToSize[block.Digest] = block.Size + } + if manifest.Err != nil { + err = manifest.Err + return } - results.UuidToCollection = make(map[string]Collection) - for _, item := range items { - item_map := item.(map[string]interface{}) - collection := Collection{Uuid: item_map["uuid"].(string), - OwnerUuid: item_map["owner_uuid"].(string), - BlockDigestToSize: make(map[string]int)} - manifest := manifest.Manifest{item_map["manifest_text"].(string)} - blockChannel := manifest.BlockIterWithDuplicates() - for block := range blockChannel { - if stored_size, stored := collection.BlockDigestToSize[block.Digest]; - stored && stored_size != block.Size { - log.Fatalf( - "Collection %s contains multiple sizes (%d and %d) for block %s", - collection.Uuid, - stored_size, - block.Size, - block.Digest) - } - collection.BlockDigestToSize[block.Digest] = block.Size + collection.TotalSize = 0 + for _, size := range collection.BlockDigestToSize { + collection.TotalSize += size + } + UUIDToCollection[collection.UUID] = collection + + // Clear out all the manifest strings that we don't need anymore. + // These hopefully form the bulk of our memory usage. + manifest.Text = "" + sdkCollection.ManifestText = "" + } + + return +} + +// Summarize the collections read +func (readCollections *ReadCollections) Summarize(arvLogger *logger.Logger) { + readCollections.OwnerToCollectionSize = make(map[string]int) + readCollections.BlockToDesiredReplication = make(map[blockdigest.DigestWithSize]int) + numCollections := len(readCollections.UUIDToCollection) + readCollections.CollectionUUIDToIndex = make(map[string]int, numCollections) + readCollections.CollectionIndexToUUID = make([]string, 0, numCollections) + readCollections.BlockToCollectionIndices = make(map[blockdigest.DigestWithSize][]int) + + for _, coll := range readCollections.UUIDToCollection { + collectionIndex := len(readCollections.CollectionIndexToUUID) + readCollections.CollectionIndexToUUID = + append(readCollections.CollectionIndexToUUID, coll.UUID) + readCollections.CollectionUUIDToIndex[coll.UUID] = collectionIndex + + readCollections.OwnerToCollectionSize[coll.OwnerUUID] = + readCollections.OwnerToCollectionSize[coll.OwnerUUID] + coll.TotalSize + + for block, size := range coll.BlockDigestToSize { + locator := blockdigest.DigestWithSize{Digest: block, Size: uint32(size)} + readCollections.BlockToCollectionIndices[locator] = + append(readCollections.BlockToCollectionIndices[locator], + collectionIndex) + storedReplication := readCollections.BlockToDesiredReplication[locator] + if coll.ReplicationLevel > storedReplication { + readCollections.BlockToDesiredReplication[locator] = + coll.ReplicationLevel } - results.UuidToCollection[collection.Uuid] = collection } } + + if arvLogger != nil { + arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) { + collectionInfo := logger.GetOrCreateMap(p, "collection_info") + // Since maps are shallow copied, we run a risk of concurrent + // updates here. By copying results.OwnerToCollectionSize into + // the log, we're assuming that it won't be updated. + collectionInfo["owner_to_collection_size"] = + readCollections.OwnerToCollectionSize + collectionInfo["distinct_blocks_named"] = + len(readCollections.BlockToDesiredReplication) + }) + } + return }