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fix: Prevent memory explosion in sqlite. And make db options configurable

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Entire-Checkpoint: e368e6d8abf3
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Jan Eitzinger
2026-03-11 06:14:05 +01:00
parent 301e590580
commit 09fa239e8b
9 changed files with 135 additions and 18 deletions
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41
.entire/logs/entire.log
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@@ -45,3 +45,44 @@
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20
cmd/cc-backend/main.go
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@@ -108,6 +108,26 @@ func initConfiguration() error {
}
func initDatabase() error {
if config.Keys.DbConfig != nil {
cfg := repository.DefaultConfig()
dc := config.Keys.DbConfig
if dc.CacheSizeMB > 0 {
cfg.DbCacheSizeMB = dc.CacheSizeMB
}
if dc.SoftHeapLimitMB > 0 {
cfg.DbSoftHeapLimitMB = dc.SoftHeapLimitMB
}
if dc.MaxOpenConnections > 0 {
cfg.MaxOpenConnections = dc.MaxOpenConnections
}
if dc.MaxIdleConnections > 0 {
cfg.MaxIdleConnections = dc.MaxIdleConnections
}
if dc.ConnectionMaxIdleTimeMins > 0 {
cfg.ConnectionMaxIdleTime = time.Duration(dc.ConnectionMaxIdleTimeMins) * time.Minute
}
repository.SetConfig(cfg)
}
repository.Connect(config.Keys.DB)
return nil
}

11
internal/config/config.go
View File

@@ -77,6 +77,17 @@ type ProgramConfig struct {
// Node state retention configuration
NodeStateRetention *NodeStateRetention `json:"nodestate-retention"`
// Database tuning configuration
DbConfig *DbConfig `json:"db-config"`
}
type DbConfig struct {
CacheSizeMB int `json:"cache-size-mb"`
SoftHeapLimitMB int `json:"soft-heap-limit-mb"`
MaxOpenConnections int `json:"max-open-connections"`
MaxIdleConnections int `json:"max-idle-connections"`
ConnectionMaxIdleTimeMins int `json:"max-idle-time-minutes"`
}
type NodeStateRetention struct {

26
internal/config/schema.go
View File

@@ -177,6 +177,32 @@ var configSchema = `
}
},
"required": ["policy"]
},
"db-config": {
"description": "SQLite database tuning configuration.",
"type": "object",
"properties": {
"cache-size-mb": {
"description": "SQLite page cache size per connection in MB (default: 2048).",
"type": "integer"
},
"soft-heap-limit-mb": {
"description": "Process-wide SQLite soft heap limit in MB (default: 16384).",
"type": "integer"
},
"max-open-connections": {
"description": "Maximum number of open database connections (default: 4).",
"type": "integer"
},
"max-idle-connections": {
"description": "Maximum number of idle database connections (default: 4).",
"type": "integer"
},
"max-idle-time-minutes": {
"description": "Maximum idle time for a connection in minutes (default: 10).",
"type": "integer"
}
}
}
}
}`

20
internal/repository/config.go
View File

@@ -27,13 +27,25 @@ type RepositoryConfig struct {
ConnectionMaxLifetime time.Duration
// ConnectionMaxIdleTime is the maximum amount of time a connection may be idle.
// Default: 1 hour
// Default: 10 minutes
ConnectionMaxIdleTime time.Duration
// MinRunningJobDuration is the minimum duration in seconds for a job to be
// considered in "running jobs" queries. This filters out very short jobs.
// Default: 600 seconds (10 minutes)
MinRunningJobDuration int
// DbCacheSizeMB is the SQLite page cache size per connection in MB.
// Uses negative PRAGMA cache_size notation (KiB). With MaxOpenConnections=4
// and DbCacheSizeMB=2048, total page cache is up to 8GB.
// Default: 2048 (2GB)
DbCacheSizeMB int
// DbSoftHeapLimitMB is the process-wide SQLite soft heap limit in MB.
// SQLite will try to release cache pages to stay under this limit.
// It's a soft limit — queries won't fail, but cache eviction becomes more aggressive.
// Default: 16384 (16GB)
DbSoftHeapLimitMB int
}
// DefaultConfig returns the default repository configuration.
@@ -44,8 +56,10 @@ func DefaultConfig() *RepositoryConfig {
MaxOpenConnections: 4,
MaxIdleConnections: 4,
ConnectionMaxLifetime: time.Hour,
ConnectionMaxIdleTime: time.Hour,
MinRunningJobDuration: 600, // 10 minutes
ConnectionMaxIdleTime: 10 * time.Minute,
MinRunningJobDuration: 600, // 10 minutes
DbCacheSizeMB: 2048, // 2GB per connection
DbSoftHeapLimitMB: 16384, // 16GB process-wide
}
}

11
internal/repository/dbConnection.go
View File

@@ -36,9 +36,10 @@ type DatabaseOptions struct {
ConnectionMaxIdleTime time.Duration
}
func setupSqlite(db *sql.DB) error {
func setupSqlite(db *sql.DB, cfg *RepositoryConfig) error {
pragmas := []string{
"temp_store = memory",
fmt.Sprintf("soft_heap_limit = %d", int64(cfg.DbSoftHeapLimitMB)*1024*1024),
}
for _, pragma := range pragmas {
@@ -79,7 +80,8 @@ func Connect(db string) {
connectionURLParams.Add("_journal_mode", "WAL")
connectionURLParams.Add("_busy_timeout", "5000")
connectionURLParams.Add("_synchronous", "NORMAL")
connectionURLParams.Add("_cache_size", "1000000000")
cacheSizeKiB := repoConfig.DbCacheSizeMB * 1024 // Convert MB to KiB
connectionURLParams.Add("_cache_size", fmt.Sprintf("-%d", cacheSizeKiB))
connectionURLParams.Add("_foreign_keys", "true")
opts.URL = fmt.Sprintf("file:%s?%s", opts.URL, connectionURLParams.Encode())
@@ -94,11 +96,14 @@ func Connect(db string) {
cclog.Abortf("DB Connection: Could not connect to SQLite database with sqlx.Open().\nError: %s\n", err.Error())
}
err = setupSqlite(dbHandle.DB)
err = setupSqlite(dbHandle.DB, repoConfig)
if err != nil {
cclog.Abortf("Failed sqlite db setup.\nError: %s\n", err.Error())
}
cclog.Infof("SQLite config: cache_size=%dMB/conn, soft_heap_limit=%dMB, max_conns=%d",
repoConfig.DbCacheSizeMB, repoConfig.DbSoftHeapLimitMB, repoConfig.MaxOpenConnections)
dbHandle.SetMaxOpenConns(opts.MaxOpenConnections)
dbHandle.SetMaxIdleConns(opts.MaxIdleConnections)
dbHandle.SetConnMaxLifetime(opts.ConnectionMaxLifetime)

4
internal/repository/jobFind.go
View File

@@ -171,7 +171,7 @@ func (r *JobRepository) FindByID(ctx context.Context, jobID int64) (*schema.Job,
return nil, qerr
}
return scanJob(q.RunWith(r.stmtCache).QueryRow())
return scanJob(q.RunWith(r.stmtCache).QueryRowContext(ctx))
}
// FindByIDWithUser executes a SQL query to find a specific batch job.
@@ -217,7 +217,7 @@ func (r *JobRepository) FindByJobID(ctx context.Context, jobID int64, startTime
return nil, qerr
}
return scanJob(q.RunWith(r.stmtCache).QueryRow())
return scanJob(q.RunWith(r.stmtCache).QueryRowContext(ctx))
}
// IsJobOwner checks if the specified user owns the batch job identified by jobID,

4
internal/repository/jobQuery.go
View File

@@ -84,7 +84,7 @@ func (r *JobRepository) QueryJobs(
query = BuildWhereClause(f, query)
}
rows, err := query.RunWith(r.stmtCache).Query()
rows, err := query.RunWith(r.stmtCache).QueryContext(ctx)
if err != nil {
queryString, queryVars, _ := query.ToSql()
return nil, fmt.Errorf("query failed [%s] %v: %w", queryString, queryVars, err)
@@ -126,7 +126,7 @@ func (r *JobRepository) CountJobs(
}
var count int
if err := query.RunWith(r.DB).Scan(&count); err != nil {
if err := query.RunWith(r.DB).QueryRowContext(ctx).Scan(&count); err != nil {
return 0, fmt.Errorf("failed to count jobs: %w", err)
}

16
internal/repository/stats.go
View File

@@ -230,7 +230,7 @@ func (r *JobRepository) JobsStatsGrouped(
query = query.Offset((uint64(page.Page) - 1) * limit).Limit(limit)
}
rows, err := query.RunWith(r.DB).Query()
rows, err := query.RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Warn("Error while querying DB for job statistics")
return nil, err
@@ -355,7 +355,7 @@ func (r *JobRepository) JobsStats(
return nil, err
}
row := query.RunWith(r.DB).QueryRow()
row := query.RunWith(r.DB).QueryRowContext(ctx)
stats := make([]*model.JobsStatistics, 0, 1)
var jobs, users, walltime, nodes, nodeHours, cores, coreHours, accs, accHours sql.NullInt64
@@ -440,7 +440,7 @@ func (r *JobRepository) JobCountGrouped(
if err != nil {
return nil, err
}
rows, err := query.RunWith(r.DB).Query()
rows, err := query.RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Warn("Error while querying DB for job statistics")
return nil, err
@@ -501,7 +501,7 @@ func (r *JobRepository) AddJobCountGrouped(
if err != nil {
return nil, err
}
rows, err := query.RunWith(r.DB).Query()
rows, err := query.RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Warn("Error while querying DB for job statistics")
return nil, err
@@ -566,7 +566,7 @@ func (r *JobRepository) AddJobCount(
return nil, err
}
var cnt sql.NullInt64
if err := query.RunWith(r.DB).QueryRow().Scan(&cnt); err != nil {
if err := query.RunWith(r.DB).QueryRowContext(ctx).Scan(&cnt); err != nil {
cclog.Warn("Error while querying DB for job count")
return nil, err
}
@@ -755,7 +755,7 @@ func (r *JobRepository) jobsStatisticsHistogram(
query = BuildWhereClause(f, query)
}
rows, err := query.GroupBy("value").RunWith(r.DB).Query()
rows, err := query.GroupBy("value").RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Error("Error while running query")
return nil, err
@@ -829,7 +829,7 @@ func (r *JobRepository) jobsDurationStatisticsHistogram(
query = BuildWhereClause(f, query)
}
rows, err := query.GroupBy("value").RunWith(r.DB).Query()
rows, err := query.GroupBy("value").RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Error("Error while running query")
return nil, err
@@ -959,7 +959,7 @@ func (r *JobRepository) jobsMetricStatisticsHistogram(
mainQuery = mainQuery.GroupBy("bin").OrderBy("bin")
rows, err := mainQuery.RunWith(r.DB).Query()
rows, err := mainQuery.RunWith(r.DB).QueryContext(ctx)
if err != nil {
cclog.Errorf("Error while running mainQuery: %s", err)
return nil, err