-/* Deals with parsing Collection responses from API Server. */
+// Deals with parsing Collection responses from API Server.
package collection
"git.curoverse.com/arvados.git/services/datamanager/loggerutil"
"log"
"os"
- "runtime"
"runtime/pprof"
"time"
)
var (
- heap_profile_filename string
+ heapProfileFilename string
// globals for debugging
totalManifestSize uint64
maxManifestSize uint64
)
+// Collection representation
type Collection struct {
- 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
+ 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
}
+// SdkCollectionInfo holds collection info from api
type SdkCollectionInfo struct {
- Uuid string `json:"uuid"`
- OwnerUuid string `json:"owner_uuid"`
+ 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(&heap_profile_filename,
+ flag.StringVar(&heapProfileFilename,
"heap-profile",
"",
"File to write the heap profiles to. Leave blank to skip profiling.")
}
-// Write the heap profile to a file for later review.
+// 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() {
- if heap_profile_filename != "" {
+ if heapProfileFilename != "" {
- heap_profile, err := os.Create(heap_profile_filename)
+ heapProfile, err := os.Create(heapProfileFilename)
if err != nil {
log.Fatal(err)
}
- defer heap_profile.Close()
+ defer heapProfile.Close()
- err = pprof.WriteHeapProfile(heap_profile)
+ err = pprof.WriteHeapProfile(heapProfile)
if err != nil {
log.Fatal(err)
}
}
}
+// GetCollectionsAndSummarize gets collections from api and summarizes
func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections) {
results = GetCollections(params)
- ComputeSizeOfOwnedCollections(&results)
-
- if params.Logger != nil {
- params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
- collectionInfo := p["collection_info"].(map[string]interface{})
- // 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"] = results.OwnerToCollectionSize
- })
- }
+ results.Summarize(params.Logger)
log.Printf("Uuid to Size used: %v", results.OwnerToCollectionSize)
log.Printf("Read and processed %d collections",
- len(results.UuidToCollection))
+ 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
return
}
+// GetCollections gets collections from api
func GetCollections(params GetCollectionsParams) (results ReadCollections) {
if ¶ms.Client == nil {
log.Fatalf("params.Client passed to GetCollections() should " +
fieldsWanted := []string{"manifest_text",
"owner_uuid",
"uuid",
- // TODO(misha): Start using the redundancy field.
"redundancy",
"modified_at"}
sdkParams["limit"] = params.BatchSize
}
+ var defaultReplicationLevel int
+ {
+ value, err := params.Client.Discovery("defaultCollectionReplication")
+ if err != nil {
+ loggerutil.FatalWithMessage(params.Logger,
+ fmt.Sprintf("Error querying default collection replication: %v", err))
+ }
+
+ defaultReplicationLevel = int(value.(float64))
+ if defaultReplicationLevel <= 0 {
+ loggerutil.FatalWithMessage(params.Logger,
+ fmt.Sprintf("Default collection replication returned by arvados SDK "+
+ "should be a positive integer but instead it was %d.",
+ defaultReplicationLevel))
+ }
+ }
+
initialNumberOfCollectionsAvailable, err :=
util.NumberItemsAvailable(params.Client, "collections")
if err != nil {
// 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.UUIDToCollection = make(map[string]Collection, maxExpectedCollections)
if params.Logger != nil {
params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
- collectionInfo := make(map[string]interface{})
+ collectionInfo := logger.GetOrCreateMap(p, "collection_info")
collectionInfo["num_collections_at_start"] = initialNumberOfCollectionsAvailable
collectionInfo["batch_size"] = params.BatchSize
- p["collection_info"] = collectionInfo
+ collectionInfo["default_replication_level"] = defaultReplicationLevel
})
}
sdkParams["filters"].([][]string)[0][2] =
ProcessCollections(params.Logger,
collections.Items,
- results.UuidToCollection).Format(time.RFC3339)
+ defaultReplicationLevel,
+ results.UUIDToCollection).Format(time.RFC3339)
// update counts
previousTotalCollections = totalCollections
- totalCollections = len(results.UuidToCollection)
+ 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",
if params.Logger != nil {
params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
- collectionInfo := p["collection_info"].(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
}
}
- // Just in case this lowers the numbers reported in the heap profile.
- runtime.GC()
-
// Write the heap profile for examining memory usage
WriteHeapProfile()
return string([]byte(s))
}
+// ProcessCollections read from api server
func ProcessCollections(arvLogger *logger.Logger,
receivedCollections []SdkCollectionInfo,
- uuidToCollection map[string]Collection) (latestModificationDate time.Time) {
+ defaultReplicationLevel int,
+ UUIDToCollection map[string]Collection) (latestModificationDate time.Time) {
for _, sdkCollection := range receivedCollections {
- collection := Collection{Uuid: StrCopy(sdkCollection.Uuid),
- OwnerUuid: StrCopy(sdkCollection.OwnerUuid),
+ collection := Collection{UUID: StrCopy(sdkCollection.UUID),
+ OwnerUUID: StrCopy(sdkCollection.OwnerUUID),
ReplicationLevel: sdkCollection.Redundancy,
BlockDigestToSize: make(map[blockdigest.BlockDigest]int)}
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf(
"Arvados SDK collection returned with unexpected zero "+
- "modifcation date. This probably means that either we failed to "+
+ "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",
+ "it returns modification dates: %+v",
collection))
}
if sdkCollection.ModifiedAt.After(latestModificationDate) {
latestModificationDate = sdkCollection.ModifiedAt
}
+
+ if collection.ReplicationLevel == 0 {
+ collection.ReplicationLevel = defaultReplicationLevel
+ }
+
manifest := manifest.Manifest{sdkCollection.ManifestText}
manifestSize := uint64(len(sdkCollection.ManifestText))
- if _, alreadySeen := uuidToCollection[collection.Uuid]; !alreadySeen {
+ if _, alreadySeen := UUIDToCollection[collection.UUID]; !alreadySeen {
totalManifestSize += manifestSize
}
if manifestSize > maxManifestSize {
blockChannel := manifest.BlockIterWithDuplicates()
for block := range blockChannel {
- if stored_size, stored := collection.BlockDigestToSize[block.Digest]; stored && stored_size != block.Size {
+ if storedSize, stored := collection.BlockDigestToSize[block.Digest]; stored && storedSize != block.Size {
message := fmt.Sprintf(
"Collection %s contains multiple sizes (%d and %d) for block %s",
- collection.Uuid,
- stored_size,
+ collection.UUID,
+ storedSize,
block.Size,
block.Digest)
loggerutil.FatalWithMessage(arvLogger, message)
for _, size := range collection.BlockDigestToSize {
collection.TotalSize += size
}
- uuidToCollection[collection.Uuid] = collection
+ 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.
return
}
-func ComputeSizeOfOwnedCollections(readCollections *ReadCollections) {
+// Summarize the collections read
+func (readCollections *ReadCollections) Summarize(arvLogger *logger.Logger) {
readCollections.OwnerToCollectionSize = make(map[string]int)
- for _, coll := range readCollections.UuidToCollection {
- readCollections.OwnerToCollectionSize[coll.OwnerUuid] =
- readCollections.OwnerToCollectionSize[coll.OwnerUuid] + coll.TotalSize
+ 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
+ }
+ }
+ }
+
+ 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