package collection
import (
+ "flag"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/blockdigest"
"git.curoverse.com/arvados.git/sdk/go/manifest"
- "git.curoverse.com/arvados.git/sdk/go/util"
+ //"git.curoverse.com/arvados.git/sdk/go/util"
"log"
+ "os"
+ "runtime/pprof"
+ "time"
+)
+
+var (
+ heap_profile_filename string
+ heap_profile *os.File
)
type Collection struct {
Uuid string
OwnerUuid string
ReplicationLevel int
- BlockDigestToSize map[string]int
+ BlockDigestToSize map[blockdigest.BlockDigest]int
TotalSize int
}
type GetCollectionsParams struct {
Client arvadosclient.ArvadosClient
- Limit int
- LogEveryNthCollectionProcessed int // 0 means don't report any
+ BatchSize int
}
type SdkCollectionInfo struct {
- Uuid string `json:"uuid"`
- OwnerUuid string `json:"owner_uuid"`
- Redundancy int `json:"redundancy"`
- ManifestText string `json:"manifest_text"`
+ Uuid string `json:"uuid"`
+ OwnerUuid string `json:"owner_uuid"`
+ Redundancy int `json:"redundancy"`
+ ModifiedAt time.Time `json:"modified_at"`
+ ManifestText string `json:"manifest_text"`
}
type SdkCollectionList struct {
Items []SdkCollectionInfo `json:"items"`
}
-// Methods to implement util.SdkListResponse Interface
-func (s SdkCollectionList) NumItemsAvailable() (numAvailable int, err error) {
- return s.ItemsAvailable, nil
+func init() {
+ flag.StringVar(&heap_profile_filename,
+ "heap-profile",
+ "",
+ "File to write the heap profiles to.")
}
-func (s SdkCollectionList) NumItemsContained() (numContained int, err error) {
- return len(s.Items), nil
-}
+// // Methods to implement util.SdkListResponse Interface
+// func (s SdkCollectionList) NumItemsAvailable() (numAvailable int, err error) {
+// return s.ItemsAvailable, nil
+// }
+
+// func (s SdkCollectionList) NumItemsContained() (numContained int, err error) {
+// return len(s.Items), nil
+// }
func GetCollections(params GetCollectionsParams) (results ReadCollections) {
if ¶ms.Client == nil {
"contain a valid ArvadosClient, but instead it is nil.")
}
+ // TODO(misha): move this code somewhere better and make sure it's
+ // only run once
+ if heap_profile_filename != "" {
+ var err error
+ heap_profile, err = os.Create(heap_profile_filename)
+ if err != nil {
+ log.Fatal(err)
+ }
+ }
+
fieldsWanted := []string{"manifest_text",
"owner_uuid",
"uuid",
// TODO(misha): Start using the redundancy field.
- "redundancy"}
-
- sdkParams := arvadosclient.Dict{"select": fieldsWanted}
- if params.Limit > 0 {
- sdkParams["limit"] = params.Limit
+ "redundancy",
+ "modified_at"}
+
+ sdkParams := arvadosclient.Dict{
+ "select": fieldsWanted,
+ "order": []string{"modified_at ASC"},
+ "filters": [][]string{[]string{"modified_at", ">=", "1900-01-01T00:00:00Z"}}}
+ // MISHA UNDO THIS TEMPORARY HACK TO FIND BUG!
+ //"filters": [][]string{[]string{"modified_at", ">=", "2014-11-05T20:44:50Z"}}}
+
+ if params.BatchSize > 0 {
+ sdkParams["limit"] = params.BatchSize
}
- var collections SdkCollectionList
- err := params.Client.List("collections", sdkParams, &collections)
- if err != nil {
- log.Fatalf("error querying collections: %v", err)
- }
-
- {
- var numReceived, numAvailable int
- results.ReadAllCollections, numReceived, numAvailable =
- util.ContainsAllAvailableItems(collections)
+ // MISHA UNDO THIS TEMPORARY HACK TO FIND BUG!
+ sdkParams["limit"] = 50
+
+ // {
+ // var numReceived, numAvailable int
+ // results.ReadAllCollections, numReceived, numAvailable =
+ // util.ContainsAllAvailableItems(collections)
+
+ // if (!results.ReadAllCollections) {
+ // log.Printf("ERROR: Did not receive all collections.")
+ // }
+ // log.Printf("Received %d of %d available collections.",
+ // numReceived,
+ // numAvailable)
+ // }
+
+ initialNumberOfCollectionsAvailable := NumberCollectionsAvailable(params.Client)
+ // 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)
+
+ previousTotalCollections := -1
+ for len(results.UuidToCollection) > previousTotalCollections {
+ // We're still finding new collections
+ log.Printf("previous, current: %d %d", previousTotalCollections, len(results.UuidToCollection))
+
+ // update count
+ previousTotalCollections = len(results.UuidToCollection)
+
+ // Write the heap profile for examining memory usage
+ if heap_profile != nil {
+ err := pprof.WriteHeapProfile(heap_profile)
+ if err != nil {
+ log.Fatal(err)
+ }
+ }
- if (!results.ReadAllCollections) {
- log.Printf("ERROR: Did not receive all collections.")
+ // Get next batch of collections.
+ var collections SdkCollectionList
+ log.Printf("Running with SDK Params: %v", sdkParams)
+ err := params.Client.List("collections", sdkParams, &collections)
+ if err != nil {
+ log.Fatalf("error querying collections: %+v", err)
}
- log.Printf("Received %d of %d available collections.",
- numReceived,
- numAvailable)
+
+ // Process collection and update our date filter.
+ sdkParams["filters"].([][]string)[0][2] =
+ ProcessCollections(collections.Items, results.UuidToCollection).Format(time.RFC3339)
+ log.Printf("Latest date seen %s", sdkParams["filters"].([][]string)[0][2])
}
+ log.Printf("previous, current: %d %d", previousTotalCollections, len(results.UuidToCollection))
- results.UuidToCollection = make(map[string]Collection)
- for i, sdkCollection := range collections.Items {
- count := i + 1
- if m := params.LogEveryNthCollectionProcessed; m >0 && (count % m) == 0 {
- log.Printf("Processing collection #%d", count)
+ // Write the heap profile for examining memory usage
+ if heap_profile != nil {
+ err := pprof.WriteHeapProfile(heap_profile)
+ if err != nil {
+ log.Fatal(err)
}
+ }
+
+ return
+}
+
+
+func ProcessCollections(receivedCollections []SdkCollectionInfo,
+ uuidToCollection map[string]Collection) (latestModificationDate time.Time) {
+ for _, sdkCollection := range receivedCollections {
collection := Collection{Uuid: sdkCollection.Uuid,
OwnerUuid: sdkCollection.OwnerUuid,
ReplicationLevel: sdkCollection.Redundancy,
- BlockDigestToSize: make(map[string]int)}
+ BlockDigestToSize: make(map[blockdigest.BlockDigest]int)}
+
+ if sdkCollection.ModifiedAt.IsZero() {
+ log.Fatalf(
+ "Arvados SDK collection returned with unexpected zero modifcation " +
+ "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
+ }
manifest := manifest.Manifest{sdkCollection.ManifestText}
blockChannel := manifest.BlockIterWithDuplicates()
for block := range blockChannel {
for _, size := range collection.BlockDigestToSize {
collection.TotalSize += size
}
- results.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.
+ manifest.Text = ""
+ sdkCollection.ManifestText = ""
}
return
}
+
+
+func NumberCollectionsAvailable(client arvadosclient.ArvadosClient) (int) {
+ var collections SdkCollectionList
+ sdkParams := arvadosclient.Dict{"limit": 0}
+ err := client.List("collections", sdkParams, &collections)
+ if err != nil {
+ log.Fatalf("error querying collections for items available: %v", err)
+ }
+
+ return collections.ItemsAvailable
+}
projects / arvados.git / blobdiff