tools/syz-covermerger: upload coverage as jsonl

Previous implementation store only the summary of processed records.
The summary was <1GB and single processing node was able to manipulate the data.

Current implementation stores all the details about records read to make post-processing more flexible.
This change was needed to get access to the source manager name and will help to analyze other details.
This new implementation requires 20GB mem to process single day records.
CSV log interning experiment allowed to merge using 10G.
Quarter data aggregation will cost ~100 times more.

The alternative is to use stream processing. We can process data kernel-file-by-file.
It allows to /15000 memory consumption.
This approach is implemented here.
We're batching coverage signals by file and store per-file results in GCS JSONL file.
See https://jsonlines.org/ to learn about jsonl.

Author: tarasmadan

dashboard/app/api.go

@@ -1938,37 +1938,27 @@ func apiCreateUploadURL(c context.Context, payload io.Reader) (interface{}, erro
 	}
 	return fmt.Printf("%s/%s.upload", bucket, uuid.New().String())
 }
+
+// apiSaveCoverage reads jsonl data from payload and stores it to coveragedb.
+// First payload jsonl line is a coveragedb.HistoryRecord (w/o session and time).
+// Second+ records are coveragedb.MergedCoverageRecord.
 func apiSaveCoverage(c context.Context, payload io.Reader) (interface{}, error) {
-	req := new(dashapi.SaveCoverageReq)
-	if err := json.NewDecoder(payload).Decode(req); err != nil {
-		return nil, fmt.Errorf("failed to unmarshal request: %w", err)
+	descr := new(coveragedb.HistoryRecord)
+	if err := json.NewDecoder(payload).Decode(descr); err != nil {
+		return 0, fmt.Errorf("json.NewDecoder(dashapi.MergedCoverageDescription).Decode: %w", err)
 	}
-	coverage := req.Coverage
 	var sss []*subsystem.Subsystem
-	if service := getNsConfig(c, coverage.Namespace).Subsystems.Service; service != nil {
+	if service := getNsConfig(c, descr.Namespace).Subsystems.Service; service != nil {
 		sss = service.List()
-		log.Infof(c, "found %d subsystems for %s namespace", len(sss), coverage.Namespace)
-	}
-	rowsCreated, err := coveragedb.SaveMergeResult(
-		context.Background(),
-		appengine.AppID(context.Background()),
-		coverage.FileData,
-		&coveragedb.HistoryRecord{
-			Namespace: coverage.Namespace,
-			Repo:      coverage.Repo,
-			Commit:    coverage.Commit,
-			Duration:  coverage.Duration,
-			DateTo:    coverage.DateTo,
-		},
-		coverage.TotalRows,
-		sss,
-	)
+		log.Infof(c, "found %d subsystems for %s namespace", len(sss), descr.Namespace)
+	}
+	rowsCreated, err := coveragedb.SaveMergeResult(c, appengine.AppID(context.Background()), descr, payload, sss)
 	if err != nil {
 		log.Errorf(c, "error storing coverage for ns %s, date %s: %v",
-			coverage.Namespace, coverage.DateTo.String(), err)
+			descr.Namespace, descr.DateTo.String(), err)
 	} else {
 		log.Infof(c, "updated coverage for ns %s, date %s to %d rows",
-			coverage.Namespace, coverage.DateTo.String(), coverage.TotalRows)
+			descr.Namespace, descr.DateTo.String(), descr.TotalRows)
 	}
 	return &rowsCreated, err
 }

dashboard/dashapi/dashapi.go

@@ -8,7 +8,6 @@ package dashapi
 import (
 	"bytes"
 	"compress/gzip"
-	"context"
 	"encoding/json"
 	"fmt"
 	"io"
@@ -18,10 +17,7 @@ import (
 	"reflect"
 	"time"
 
-	"cloud.google.com/go/civil"
 	"github.com/google/syzkaller/pkg/auth"
-	"github.com/google/syzkaller/pkg/coveragedb"
-	"github.com/google/syzkaller/pkg/gcs"
 )
 
 type Dashboard struct {
@@ -692,42 +688,18 @@ func (dash *Dashboard) SaveDiscussion(req *SaveDiscussionReq) error {
 	return dash.Query("save_discussion", req, nil)
 }
 
-type MergedCoverage struct {
-	Namespace string
-	Repo      string
-	Commit    string
-	Duration  int64
-	DateTo    civil.Date
-	TotalRows int64
-	FileData  coveragedb.ManagersCoverage
-}
-
-type SaveCoverageReq struct {
-	Coverage *MergedCoverage
-}
-
-// SaveCoverage returns amount of records created in db.
-func (dash *Dashboard) SaveCoverage(req *SaveCoverageReq) (int, error) {
+func (dash *Dashboard) CreateUploadURL() (string, error) {
 	uploadURL := new(string)
-	if err := dash.Query("create_upload_url", req, uploadURL); err != nil {
-		return 0, fmt.Errorf("create_upload_url: %w", err)
-	}
-
-	gcsClient, err := gcs.NewClient(context.Background())
-	if err != nil {
-		return 0, fmt.Errorf("gcs.NewClient: %w", err)
-	}
-	w, err := gcsClient.FileWriter(*uploadURL)
-	if err != nil {
-		return 0, fmt.Errorf("gcsClient.FileWriter: %w", err)
-	}
-	defer w.Close()
-	if err := json.NewEncoder(gzip.NewWriter(w)).Encode(req); err != nil {
-		return 0, fmt.Errorf("json.NewEncoder(gzip.NewWriter(w)).Encode: %w", err)
+	if err := dash.Query("create_upload_url", nil, uploadURL); err != nil {
+		return "", fmt.Errorf("create_upload_url: %w", err)
 	}
+	return *uploadURL, nil
+}
 
+// SaveCoverage returns amount of records created in db.
+func (dash *Dashboard) SaveCoverage(gcpURL string) (int, error) {
 	rowsWritten := new(int)
-	if err := dash.Query("save_coverage", *uploadURL, rowsWritten); err != nil {
+	if err := dash.Query("save_coverage", gcpURL, rowsWritten); err != nil {
 		return 0, fmt.Errorf("save_coverage: %w", err)
 	}
 	return *rowsWritten, nil

pkg/cover/file.go

@@ -78,14 +78,24 @@ func GetMergeResult(c context.Context, ns, repo, forCommit, sourceCommit, filePa
 		return nil, fmt.Errorf("failed to dbReader.Reader: %w", err)
 	}
 
-	mergeResult, err := covermerger.MergeCSVData(config, csvReader)
-	if err != nil {
+	ch := make(chan *covermerger.FileMergeResult, 1)
+	if err := covermerger.MergeCSVData(config, csvReader, ch); err != nil {
 		return nil, fmt.Errorf("error merging coverage: %w", err)
 	}
-	if _, exist := mergeResult[filePath]; !exist {
+
+	var mr *covermerger.MergeResult
+	select {
+	case fmr := <-ch:
+		if fmr != nil {
+			mr = fmr.MergeResult
+		}
+	default:
+	}
+
+	if mr != nil {
 		return nil, fmt.Errorf("no merge result for file %s", filePath)
 	}
-	return mergeResult[filePath], nil
+	return mr, nil
 }
 
 func rendResult(content string, coverage *covermerger.MergeResult, renderConfig *CoverageRenderConfig) string {

pkg/coveragedb/spanner.go

@@ -4,8 +4,11 @@
 package coveragedb
 
 import (
+	"bufio"
 	"context"
+	"encoding/json"
 	"fmt"
+	"io"
 	"os"
 	"sync/atomic"
 	"time"
@@ -51,11 +54,6 @@ func NewClient(ctx context.Context, projectID string) (*spanner.Client, error) {
 	return spanner.NewClient(ctx, database)
 }
 
-type ManagersCoverage map[string]ManagerCoverage
-
-// ManagerCoverage is a file to coverage mapping.
-type ManagerCoverage map[string]*Coverage
-
 type Coverage struct {
 	Instrumented      int64
 	Covered           int64
@@ -72,8 +70,14 @@ func (c *Coverage) AddLineHitCount(line, hitCount int) {
 	}
 }
 
-func SaveMergeResult(ctx context.Context, projectID string, manCovMap ManagersCoverage,
-	template *HistoryRecord, totalRows int64, sss []*subsystem.Subsystem) (int, error) {
+type MergedCoverageRecord struct {
+	Manager  string
+	FilePath string
+	FileData *Coverage
+}
+
+func SaveMergeResult(ctx context.Context, projectID string, descr *HistoryRecord, jsonl io.Reader,
+	sss []*subsystem.Subsystem) (int, error) {
 	client, err := NewClient(ctx, projectID)
 	if err != nil {
 		return 0, fmt.Errorf("spanner.NewClient() failed: %s", err.Error())
@@ -87,25 +91,30 @@ func SaveMergeResult(ctx context.Context, projectID string, manCovMap ManagersCo
 	session := uuid.New().String()
 	mutations := []*spanner.Mutation{}
 
-	for manager, covMap := range manCovMap {
-		for filePath, record := range covMap {
-			mutations = append(mutations, fileRecordMutation(session, manager, filePath, record))
-			subsystems := fileSubsystems(filePath, ssMatcher, ssCache)
-			mutations = append(mutations, fileSubsystemsMutation(template.Namespace, filePath, subsystems))
-			// There is a limit on the number of mutations per transaction (80k) imposed by the DB.
-			// This includes both explicit mutations of the fields (6 fields * 1k records = 6k mutations)
-			//   and implicit index mutations.
-			// We keep the number of records low enough for the number of explicit mutations * 10 does not exceed the limit.
-			if len(mutations) > 1000 {
-				if _, err = client.Apply(ctx, mutations); err != nil {
-					return rowsCreated, fmt.Errorf("failed to spanner.Apply(inserts): %s", err.Error())
-				}
-				rowsCreated += len(mutations)
-				mutations = nil
+	jsonlScanner := bufio.NewScanner(jsonl)
+
+	for jsonlScanner.Scan() {
+		var mcr MergedCoverageRecord
+		if err := json.Unmarshal([]byte(jsonlScanner.Text()), &mcr); err != nil {
+			return rowsCreated, fmt.Errorf("json.Unmarshal(MergedCoverageRecord): %w", err)
+		}
+		mutations = append(mutations, fileRecordMutation(session, &mcr))
+		subsystems := fileSubsystems(mcr.FilePath, ssMatcher, ssCache)
+		mutations = append(mutations, fileSubsystemsMutation(descr.Namespace, mcr.FilePath, subsystems))
+		// There is a limit on the number of mutations per transaction (80k) imposed by the DB.
+		// This includes both explicit mutations of the fields (6 fields * 1k records = 6k mutations)
+		//   and implicit index mutations.
+		// We keep the number of records low enough for the number of explicit mutations * 10 does not exceed the limit.
+		if len(mutations) > 1000 {
+			if _, err = client.Apply(ctx, mutations); err != nil {
+				return rowsCreated, fmt.Errorf("failed to spanner.Apply(inserts): %s", err.Error())
 			}
+			rowsCreated += len(mutations)
+			mutations = nil
 		}
 	}
-	mutations = append(mutations, historyMutation(session, template, totalRows))
+
+	mutations = append(mutations, historyMutation(session, descr))
 	if _, err = client.Apply(ctx, mutations); err != nil {
 		return rowsCreated, fmt.Errorf("failed to spanner.Apply(inserts): %s", err.Error())
 	}
@@ -170,7 +179,7 @@ func ReadLinesHitCount(ctx context.Context, ns, commit, file string, tp TimePeri
 	return res, nil
 }
 
-func historyMutation(session string, template *HistoryRecord, totalRows int64) *spanner.Mutation {
+func historyMutation(session string, template *HistoryRecord) *spanner.Mutation {
 	historyInsert, err := spanner.InsertOrUpdateStruct("merge_history", &HistoryRecord{
 		Session:   session,
 		Time:      time.Now(),
@@ -179,23 +188,23 @@ func historyMutation(session string, template *HistoryRecord, totalRows int64) *
 		Commit:    template.Commit,
 		Duration:  template.Duration,
 		DateTo:    template.DateTo,
-		TotalRows: totalRows,
+		TotalRows: template.TotalRows,
 	})
 	if err != nil {
 		panic(fmt.Sprintf("failed to spanner.InsertStruct(): %s", err.Error()))
 	}
 	return historyInsert
 }
 
-func fileRecordMutation(session, manager, filePath string, record *Coverage) *spanner.Mutation {
+func fileRecordMutation(session string, mcr *MergedCoverageRecord) *spanner.Mutation {
 	insert, err := spanner.InsertOrUpdateStruct("files", &FilesRecord{
 		Session:           session,
-		FilePath:          filePath,
-		Instrumented:      record.Instrumented,
-		Covered:           record.Covered,
-		LinesInstrumented: record.LinesInstrumented,
-		HitCounts:         record.HitCounts,
-		Manager:           manager,
+		FilePath:          mcr.FilePath,
+		Instrumented:      mcr.FileData.Instrumented,
+		Covered:           mcr.FileData.Covered,
+		LinesInstrumented: mcr.FileData.LinesInstrumented,
+		HitCounts:         mcr.FileData.HitCounts,
+		Manager:           mcr.Manager,
 	})
 	if err != nil {
 		panic(fmt.Sprintf("failed to fileRecordMutation: %v", err))

pkg/covermerger/covermerger.go

@@ -10,7 +10,6 @@ import (
 	"fmt"
 	"io"
 	"strconv"
-	"sync"
 
 	"github.com/google/syzkaller/pkg/log"
 	"golang.org/x/exp/maps"
@@ -127,13 +126,16 @@ func isSchema(fields, schema []string) bool {
 	return true
 }
 
-type FilesMergeResults map[string]*MergeResult
+type FileMergeResult struct {
+	FilePath string
+	*MergeResult
+}
 
-func MergeCSVData(config *Config, reader io.Reader) (FilesMergeResults, error) {
+func MergeCSVData(config *Config, reader io.Reader, results chan<- *FileMergeResult) error {
 	var schema []string
 	csvReader := csv.NewReader(reader)
 	if fields, err := csvReader.Read(); err != nil {
-		return nil, fmt.Errorf("failed to read schema: %w", err)
+		return fmt.Errorf("failed to read schema: %w", err)
 	} else {
 		schema = fields
 	}
@@ -163,47 +165,40 @@ func MergeCSVData(config *Config, reader io.Reader) (FilesMergeResults, error) {
 		}
 		errStreamChan <- nil
 	}()
-	mergeResult, errMerging := mergeChanData(config, recordsChan)
+	errMerging := mergeChanData(config, recordsChan, results)
 	errStream := <-errStreamChan
 	if errMerging != nil || errStream != nil {
-		return nil, fmt.Errorf("errors merging stream data:\nmerger err: %w\nstream reader err: %w",
+		return fmt.Errorf("errors merging stream data:\nmerger err: %w\nstream reader err: %w",
 			errMerging, errStream)
 	}
-	return mergeResult, nil
+	return nil
 }
 
 type FileRecords struct {
 	fileName string
 	records  []*FileRecord
 }
 
-func mergeChanData(c *Config, recordChan <-chan *FileRecord) (FilesMergeResults, error) {
+func mergeChanData(c *Config, recordChan <-chan *FileRecord, results chan<- *FileMergeResult) error {
 	g, ctx := errgroup.WithContext(context.Background())
 	frecordChan := groupFileRecords(recordChan, ctx)
-	stat := make(FilesMergeResults)
-	var mu sync.Mutex
+
 	for i := 0; i < c.Jobs; i++ {
 		g.Go(func() error {
 			for frecord := range frecordChan {
-				if mr, err := batchFileData(c, frecord.fileName, frecord.records); err != nil {
+				mr, err := batchFileData(c, frecord.fileName, frecord.records)
+				if err != nil {
 					return fmt.Errorf("failed to batchFileData(%s): %w", frecord.fileName, err)
-				} else {
-					mu.Lock()
-					if _, exist := stat[frecord.fileName]; exist {
-						mu.Unlock()
-						return fmt.Errorf("file %s was already processed", frecord.fileName)
-					}
-					stat[frecord.fileName] = mr
-					mu.Unlock()
+				}
+				results <- &FileMergeResult{
+					FilePath:    frecord.fileName,
+					MergeResult: mr,
 				}
 			}
 			return nil
 		})
 	}
-	if err := g.Wait(); err != nil {
-		return nil, err
-	}
-	return stat, nil
+	return g.Wait()
 }
 
 func groupFileRecords(recordChan <-chan *FileRecord, ctx context.Context) chan FileRecords {