-/* Deals with parsing Collection responses from API Server. */
+// Deals with parsing Collection responses from API Server.
package collection
import (
- "errors"
+ "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
+)
+
+// 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
}
+// 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
+
+ return nil
}
-func IterateSdkListItems(response map[string]interface{}) (c <-chan map[string]interface{}, err error) {
- if value, ok := response["items"]; ok {
- ch := make(chan map[string]interface{})
- c = ch
- items := value.([]interface{})
- go func() {
- for _, item := range items {
- ch <- item.(map[string]interface{})
- }
- close(ch)
- }()
- } else {
- err = errors.New("Could not find \"items\" field in response " +
- "passed to IterateSdkListItems()")
+// GetCollectionsAndSummarize gets collections from api and summarizes
+func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections, err error) {
+ results, err = GetCollections(params)
+ if err != nil {
+ return
}
- 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"}},
+ "offset": 0}
+
+ 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.
+ remainingCollections := 1
+ var totalCollections int
+ var previousTotalCollections int
+ for remainingCollections > 0 {
+ // We're still finding new collections
- if (!results.ReadAllCollections) {
- log.Printf("ERROR: Did not receive all 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
+ }
+
+ // Update count of remaining collections
+ remainingCollections = collections.ItemsAvailable - params.BatchSize - sdkParams["offset"].(int)
+ if remainingCollections < 0 {
+ remainingCollections = 0
+ }
+
+ // 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
+ }
+ if sdkParams["filters"].([][]string)[0][2] != latestModificationDate.Format(time.RFC3339) {
+ sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339)
+ sdkParams["offset"] = 0
+ } else {
+ sdkParams["offset"] = sdkParams["offset"].(int) + params.BatchSize
+ }
+
+ // update counts
+ previousTotalCollections = totalCollections
+ totalCollections = len(results.UUIDToCollection)
+
+ log.Printf("%d collections read, %d new in last batch, "+
+ "%d remaining, "+
+ "%s latest modified date, %.0f %d %d avg,max,total manifest size",
+ totalCollections,
+ totalCollections-previousTotalCollections,
+ remainingCollections,
+ 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
+ })
}
- log.Printf("Received %d of %d available collections.",
- numReceived,
- numAvailable)
}
- if collectionChannel, err := IterateSdkListItems(collections); err != nil {
- log.Fatalf("Error trying to iterate collections returned by SDK: %v", err)
- } else {
- index := 0
- results.UuidToCollection = make(map[string]Collection)
- for item_map := range collectionChannel {
- index += 1
- if m := params.LogEveryNthCollectionProcessed; m >0 && (index % m) == 0 {
- log.Printf("Processing collection #%d", index)
+ // 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(
+ "Collection %s contains multiple sizes (%d and %d) for block %s",
+ collection.UUID,
+ storedSize,
+ block.Size,
+ block.Digest)
}
- 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
}
projects / arvados.git / blobdiff