X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ffb5d12c1670a1dd8f86eca7e80283b0c37a8656..779e41aaaa1f4d3a696a63011c00648bfbfaae72:/services/datamanager/collection/collection.go?ds=sidebyside diff --git a/services/datamanager/collection/collection.go b/services/datamanager/collection/collection.go index 9dc5a70202..df6852687a 100644 --- a/services/datamanager/collection/collection.go +++ b/services/datamanager/collection/collection.go @@ -1,116 +1,365 @@ -/* 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/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 + // globals for debugging + totalManifestSize uint64 + maxManifestSize uint64 +) + +// 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 + 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 + Err error } +// GetCollectionsParams params type GetCollectionsParams struct { - Client arvadosclient.ArvadosClient - Limit int - LogEveryNthCollectionProcessed int // 0 means don't report any + Client arvadosclient.ArvadosClient + Logger *logger.Logger + BatchSize int } -// TODO(misha): Move this method somewhere more central -func SdkListResponseContainsAllAvailableItems(response map[string]interface{}) (containsAll bool, numContained int, numAvailable int) { - if value, ok := response["items"]; ok { - items := value.([]interface{}) - { - var itemsAvailable interface{} - if itemsAvailable, ok = response["items_available"]; !ok { - // TODO(misha): Consider returning an error here (and above if - // we can't find items) so that callers can recover. - log.Fatalf("API server did not return the number of items available") - } - numContained = len(items) - numAvailable = int(itemsAvailable.(float64)) - // If we never entered this block, allAvailable would be false by - // default, which is what we want - containsAll = numContained == numAvailable +// 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) { + results, err := GetCollections(params) + if err != nil { + results.Err = err + 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(params GetCollectionsParams) (results ReadCollections) { +// GetCollections gets collections from api +func GetCollections(params GetCollectionsParams) (results ReadCollections, err error) { if ¶ms.Client == nil { - log.Fatalf("Received params.Client passed to GetCollections() should " + + 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"}}} + + if params.BatchSize > 0 { + sdkParams["limit"] = params.BatchSize + } - sdkParams := arvadosclient.Dict{"select": fieldsWanted} - if params.Limit > 0 { - sdkParams["limit"] = params.Limit + var defaultReplicationLevel int + { + var value interface{} + value, err = params.Client.Discovery("defaultCollectionReplication") + if err != nil { + return + } + + 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 + } } - var collections map[string]interface{} - err := params.Client.List("collections", sdkParams, &collections) + 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) - { - var numReceived, numAvailable int - results.ReadAllCollections, numReceived, numAvailable = - SdkListResponseContainsAllAvailableItems(collections) + 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 + }) + } + + // 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 + + // 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. + var latestModificationDate time.Time + latestModificationDate, err = ProcessCollections(params.Logger, + collections.Items, + defaultReplicationLevel, + results.UUIDToCollection) + if err != nil { + return + } + sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339) + + // 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 (!results.ReadAllCollections) { - log.Printf("ERROR: Did not receive all collections.") + 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 + }) } - log.Printf("Received %d of %d available collections.", - numReceived, - numAvailable) } - if value, ok := collections["items"]; ok { - items := value.([]interface{}) + // 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, 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)} - results.UuidToCollection = make(map[string]Collection) - for index, item := range items { - if m := params.LogEveryNthCollectionProcessed; m >0 && (index % m) == 0 { - log.Printf("Processing collection #%d", index) + if sdkCollection.ModifiedAt.IsZero() { + return latestModificationDate, 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) + } + + 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 { + err = fmt.Errorf( + "Collection %s contains multiple sizes (%d and %d) for block %s", + collection.UUID, + storedSize, + block.Size, + block.Digest) + return } - 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.BlockDigestToSize[block.Digest] = block.Size + } + if manifest.Err != nil { + err = manifest.Err + return + } + + 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 }