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Add cron method to gc LFS MetaObjects (#22385) 

This PR adds a task to the cron service to allow garbage collection of
LFS meta objects. As repositories may have a large number of
LFSMetaObjects, an updated column is added to this table and it is used
to perform a generational GC to attempt to reduce the amount of work.
(There may need to be a bit more work here but this is probably enough
for the moment.)

Fix #7045

Signed-off-by: Andrew Thornton <art27@cantab.net>
This commit is contained in:
zeripath 2023-01-16 19:50:53 +00:00 committed by GitHub
parent 04c97aa364
commit 2cc3a6381c
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
9 changed files with 255 additions and 35 deletions
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22
custom/conf/app.example.ini
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@ -2213,6 +2213,28 @@ ROUTER = console
;SCHEDULE = @every 168h
;OLDER_THAN = 8760h
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Garbage collect LFS pointers in repositories
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;[cron.gc_lfs]
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;ENABLED = false
;; Garbage collect LFS pointers in repositories (default false)
;RUN_AT_START = false
;; Interval as a duration between each gc run (default every 24h)
;SCHEDULE = @every 24h
;; Only attempt to garbage collect LFSMetaObjects older than this (default 7 days)
;OLDER_THAN = 168h
;; Only attempt to garbage collect LFSMetaObjects that have not been attempted to be garbage collected for this long (default 3 days)
;LAST_UPDATED_MORE_THAN_AGO = 72h
; Minimum number of stale LFSMetaObjects to check per repo. Set to `0` to always check all.
;NUMBER_TO_CHECK_PER_REPO = 100
;Check at least this proportion of LFSMetaObjects per repo. (This may cause all stale LFSMetaObjects to be checked.)
;PROPORTION_TO_CHECK_PER_REPO = 0.6
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Git Operation timeout in seconds

10
docs/content/doc/advanced/config-cheat-sheet.en-us.md
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@ -1039,6 +1039,16 @@ Default templates for project boards:
- `SCHEDULE`: **@every 168h**: Cron syntax to set how often to check.
- `OLDER_THAN`: **@every 8760h**: any system notice older than this expression will be deleted from database.
#### Cron - Garbage collect LFS pointers in repositories ('cron.gc_lfs')
- `ENABLED`: **false**: Enable service.
- `RUN_AT_START`: **false**: Run tasks at start up time (if ENABLED).
- `SCHEDULE`: **@every 24h**: Cron syntax to set how often to check.
- `OLDER_THAN`: **168h**: Only attempt to garbage collect LFSMetaObjects older than this (default 7 days)
- `LAST_UPDATED_MORE_THAN_AGO`: **72h**: Only attempt to garbage collect LFSMetaObjects that have not been attempted to be garbage collected for this long (default 3 days)
- `NUMBER_TO_CHECK_PER_REPO`: **100**: Minimum number of stale LFSMetaObjects to check per repo. Set to `0` to always check all.
- `PROPORTION_TO_CHECK_PER_REPO`: **0.6**: Check at least this proportion of LFSMetaObjects per repo. (This may cause all stale LFSMetaObjects to be checked.)
## Git (`git`)
- `PATH`: **""**: The path of Git executable. If empty, Gitea searches through the PATH environment.

69
models/git/lfs.go
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@ -115,6 +115,7 @@ type LFSMetaObject struct {
RepositoryID int64 `xorm:"UNIQUE(s) INDEX NOT NULL"`
Existing bool `xorm:"-"`
CreatedUnix timeutil.TimeStamp `xorm:"created"`
UpdatedUnix timeutil.TimeStamp `xorm:"INDEX updated"`
}
func init() {
@ -334,8 +335,45 @@ func GetRepoLFSSize(ctx context.Context, repoID int64) (int64, error) {
return lfsSize, nil
}
// IterateRepositoryIDsWithLFSMetaObjects iterates across the repositories that have LFSMetaObjects
func IterateRepositoryIDsWithLFSMetaObjects(ctx context.Context, f func(ctx context.Context, repoID, count int64) error) error {
batchSize := setting.Database.IterateBufferSize
sess := db.GetEngine(ctx)
id := int64(0)
type RepositoryCount struct {
RepositoryID int64
Count int64
}
for {
counts := make([]*RepositoryCount, 0, batchSize)
sess.Select("repository_id, COUNT(id) AS count").
Table("lfs_meta_object").
Where("repository_id > ?", id).
GroupBy("repository_id").
OrderBy("repository_id ASC")
if err := sess.Limit(batchSize, 0).Find(&counts); err != nil {
return err
}
if len(counts) == 0 {
return nil
}
for _, count := range counts {
if err := f(ctx, count.RepositoryID, count.Count); err != nil {
return err
}
}
id = counts[len(counts)-1].RepositoryID
}
}
// IterateLFSMetaObjectsForRepoOptions provides options for IterateLFSMetaObjectsForRepo
type IterateLFSMetaObjectsForRepoOptions struct {
OlderThan time.Time
OlderThan time.Time
UpdatedLessRecentlyThan time.Time
OrderByUpdated bool
LoopFunctionAlwaysUpdates bool
}
// IterateLFSMetaObjectsForRepo provides a iterator for LFSMetaObjects per Repo
@ -348,28 +386,53 @@ func IterateLFSMetaObjectsForRepo(ctx context.Context, repoID int64, f func(cont
LFSMetaObject
}
id := int64(0)
for {
beans := make([]*CountLFSMetaObject, 0, batchSize)
// SELECT `lfs_meta_object`.*, COUNT(`l1`.id) as `count` FROM lfs_meta_object INNER JOIN lfs_meta_object AS l1 ON l1.oid = lfs_meta_object.oid WHERE lfs_meta_object.repository_id = ? GROUP BY lfs_meta_object.id
sess := engine.Select("`lfs_meta_object`.*, COUNT(`l1`.oid) AS `count`").
Join("INNER", "`lfs_meta_object` AS l1", "`lfs_meta_object`.oid = `l1`.oid").
Where("`lfs_meta_object`.repository_id = ?", repoID)
if !opts.OlderThan.IsZero() {
sess.And("`lfs_meta_object`.created_unix < ?", opts.OlderThan)
}
if !opts.UpdatedLessRecentlyThan.IsZero() {
sess.And("`lfs_meta_object`.updated_unix < ?", opts.UpdatedLessRecentlyThan)
}
sess.GroupBy("`lfs_meta_object`.id")
if opts.OrderByUpdated {
sess.OrderBy("`lfs_meta_object`.updated_unix ASC")
} else {
sess.And("`lfs_meta_object`.id > ?", id)
sess.OrderBy("`lfs_meta_object`.id ASC")
}
if err := sess.Limit(batchSize, start).Find(&beans); err != nil {
return err
}
if len(beans) == 0 {
return nil
}
start += len(beans)
if !opts.LoopFunctionAlwaysUpdates {
start += len(beans)
}
for _, bean := range beans {
if err := f(ctx, &bean.LFSMetaObject, bean.Count); err != nil {
return err
}
}
id = beans[len(beans)-1].ID
}
}
// MarkLFSMetaObject updates the updated time for the provided LFSMetaObject
func MarkLFSMetaObject(ctx context.Context, id int64) error {
obj := &LFSMetaObject{
UpdatedUnix: timeutil.TimeStampNow(),
}
count, err := db.GetEngine(ctx).ID(id).Update(obj)
if count != 1 {
log.Error("Unexpectedly updated %d LFSMetaObjects with ID: %d", count, id)
}
return err
}

5
models/migrations/migrations.go
View File

@ -432,6 +432,9 @@ var migrations = []Migration{
NewMigration("Update counts of all open milestones", v1_18.UpdateOpenMilestoneCounts),
// v230 -> v231
NewMigration("Add ConfidentialClient column (default true) to OAuth2Application table", v1_18.AddConfidentialClientColumnToOAuth2ApplicationTable),
// Gitea 1.18.0 ends at v231
// v231 -> v232
NewMigration("Add index for hook_task", v1_19.AddIndexForHookTask),
// v232 -> v233
@ -446,6 +449,8 @@ var migrations = []Migration{
NewMigration("Create secrets table", v1_19.CreateSecretsTable),
// v237 -> v238
NewMigration("Drop ForeignReference table", v1_19.DropForeignReferenceTable),
// v238 -> v239
NewMigration("Add updated unix to LFSMetaObject", v1_19.AddUpdatedUnixToLFSMetaObject),
}
// GetCurrentDBVersion returns the current db version

27
models/migrations/v1_19/v238.go Normal file
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@ -0,0 +1,27 @@
// Copyright 2022 The Gitea Authors. All rights reserved.
// SPDX-License-Identifier: MIT
package v1_19 //nolint
import (
"code.gitea.io/gitea/modules/timeutil"
"xorm.io/xorm"
)
// AddUpdatedUnixToLFSMetaObject adds an updated column to the LFSMetaObject to allow for garbage collection
func AddUpdatedUnixToLFSMetaObject(x *xorm.Engine) error {
// Drop the table introduced in `v211`, it's considered badly designed and doesn't look like to be used.
// See: https://github.com/go-gitea/gitea/issues/21086#issuecomment-1318217453
// LFSMetaObject stores metadata for LFS tracked files.
type LFSMetaObject struct {
ID int64 `xorm:"pk autoincr"`
Oid string `json:"oid" xorm:"UNIQUE(s) INDEX NOT NULL"`
Size int64 `json:"size" xorm:"NOT NULL"`
RepositoryID int64 `xorm:"UNIQUE(s) INDEX NOT NULL"`
CreatedUnix timeutil.TimeStamp `xorm:"created"`
UpdatedUnix timeutil.TimeStamp `xorm:"INDEX updated"`
}
return x.Sync(new(LFSMetaObject))
}

16
modules/doctor/lfs.go
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@ -6,6 +6,7 @@ package doctor
import (
"context"
"fmt"
"time"
"code.gitea.io/gitea/modules/log"
"code.gitea.io/gitea/modules/setting"
@ -29,7 +30,20 @@ func garbageCollectLFSCheck(ctx context.Context, logger log.Logger, autofix bool
return fmt.Errorf("LFS support is disabled")
}
if err := repository.GarbageCollectLFSMetaObjects(ctx, logger, autofix); err != nil {
if err := repository.GarbageCollectLFSMetaObjects(ctx, repository.GarbageCollectLFSMetaObjectsOptions{
Logger: logger,
AutoFix: autofix,
// Only attempt to garbage collect lfs meta objects older than a week as the order of git lfs upload
// and git object upload is not necessarily guaranteed. It's possible to imagine a situation whereby
// an LFS object is uploaded but the git branch is not uploaded immediately, or there are some rapid
// changes in new branches that might lead to lfs objects becoming temporarily unassociated with git
// objects.
//
// It is likely that a week is potentially excessive but it should definitely be enough that any
// unassociated LFS object is genuinely unassociated.
OlderThan: time.Now().Add(-24 * time.Hour * 7),
// We don't set the UpdatedLessRecentlyThan because we want to do a full GC
}); err != nil {
return err
}

1
options/locale/locale_en-US.ini
View File

@ -2554,6 +2554,7 @@ dashboard.delete_old_actions = Delete all old actions from database
dashboard.delete_old_actions.started = Delete all old actions from database started.
dashboard.update_checker = Update checker
dashboard.delete_old_system_notices = Delete all old system notices from database
dashboard.gc_lfs = Garbage collect LFS meta objects
users.user_manage_panel = User Account Management
users.new_account = Create User Account

43
services/cron/tasks_extended.go
View File

@ -175,6 +175,48 @@ func registerDeleteOldSystemNotices() {
})
}
func registerGCLFS() {
if !setting.LFS.StartServer {
return
}
type GCLFSConfig struct {
OlderThanConfig
LastUpdatedMoreThanAgo time.Duration
NumberToCheckPerRepo int64
ProportionToCheckPerRepo float64
}
RegisterTaskFatal("gc_lfs", &GCLFSConfig{
OlderThanConfig: OlderThanConfig{
BaseConfig: BaseConfig{
Enabled: false,
RunAtStart: false,
Schedule: "@every 24h",
},
// Only attempt to garbage collect lfs meta objects older than a week as the order of git lfs upload
// and git object upload is not necessarily guaranteed. It's possible to imagine a situation whereby
// an LFS object is uploaded but the git branch is not uploaded immediately, or there are some rapid
// changes in new branches that might lead to lfs objects becoming temporarily unassociated with git
// objects.
//
// It is likely that a week is potentially excessive but it should definitely be enough that any
// unassociated LFS object is genuinely unassociated.
OlderThan: 24 * time.Hour * 7,
},
// Only GC things that haven't been looked at in the past 3 days
LastUpdatedMoreThanAgo: 24 * time.Hour * 3,
NumberToCheckPerRepo: 100,
ProportionToCheckPerRepo: 0.6,
}, func(ctx context.Context, _ *user_model.User, config Config) error {
gcLFSConfig := config.(*GCLFSConfig)
return repo_service.GarbageCollectLFSMetaObjects(ctx, repo_service.GarbageCollectLFSMetaObjectsOptions{
AutoFix: true,
OlderThan: time.Now().Add(-gcLFSConfig.OlderThan),
UpdatedLessRecentlyThan: time.Now().Add(-gcLFSConfig.LastUpdatedMoreThanAgo),
})
})
}
func initExtendedTasks() {
registerDeleteInactiveUsers()
registerDeleteRepositoryArchives()
@ -188,4 +230,5 @@ func initExtendedTasks() {
registerDeleteOldActions()
registerUpdateGiteaChecker()
registerDeleteOldSystemNotices()
registerGCLFS()
}

97
services/repository/lfs.go
View File

@ -5,49 +5,67 @@ package repository
import (
"context"
"errors"
"fmt"
"time"
"code.gitea.io/gitea/models/db"
git_model "code.gitea.io/gitea/models/git"
repo_model "code.gitea.io/gitea/models/repo"
"code.gitea.io/gitea/modules/git"
"code.gitea.io/gitea/modules/lfs"
"code.gitea.io/gitea/modules/log"
"xorm.io/builder"
"code.gitea.io/gitea/modules/setting"
)
func GarbageCollectLFSMetaObjects(ctx context.Context, logger log.Logger, autofix bool) error {
log.Trace("Doing: GarbageCollectLFSMetaObjects")
if err := db.Iterate(
ctx,
builder.And(builder.Gt{"id": 0}),
func(ctx context.Context, repo *repo_model.Repository) error {
return GarbageCollectLFSMetaObjectsForRepo(ctx, repo, logger, autofix)
},
); err != nil {
return err
}
log.Trace("Finished: GarbageCollectLFSMetaObjects")
return nil
// GarbageCollectLFSMetaObjectsOptions provides options for GarbageCollectLFSMetaObjects function
type GarbageCollectLFSMetaObjectsOptions struct {
Logger log.Logger
AutoFix bool
OlderThan time.Time
UpdatedLessRecentlyThan time.Time
NumberToCheckPerRepo int64
ProportionToCheckPerRepo float64
}
func GarbageCollectLFSMetaObjectsForRepo(ctx context.Context, repo *repo_model.Repository, logger log.Logger, autofix bool) error {
if logger != nil {
logger.Info("Checking %-v", repo)
// GarbageCollectLFSMetaObjects garbage collects LFS objects for all repositories
func GarbageCollectLFSMetaObjects(ctx context.Context, opts GarbageCollectLFSMetaObjectsOptions) error {
log.Trace("Doing: GarbageCollectLFSMetaObjects")
defer log.Trace("Finished: GarbageCollectLFSMetaObjects")
if !setting.LFS.StartServer {
if opts.Logger != nil {
opts.Logger.Info("LFS support is disabled")
}
return nil
}
total, orphaned, collected, deleted := 0, 0, 0, 0
if logger != nil {
return git_model.IterateRepositoryIDsWithLFSMetaObjects(ctx, func(ctx context.Context, repoID, count int64) error {
repo, err := repo_model.GetRepositoryByID(ctx, repoID)
if err != nil {
return err
}
if newMinimum := int64(float64(count) * opts.ProportionToCheckPerRepo); newMinimum > opts.NumberToCheckPerRepo && opts.NumberToCheckPerRepo != 0 {
opts.NumberToCheckPerRepo = newMinimum
}
return GarbageCollectLFSMetaObjectsForRepo(ctx, repo, opts)
})
}
// GarbageCollectLFSMetaObjectsForRepo garbage collects LFS objects for a specific repository
func GarbageCollectLFSMetaObjectsForRepo(ctx context.Context, repo *repo_model.Repository, opts GarbageCollectLFSMetaObjectsOptions) error {
if opts.Logger != nil {
opts.Logger.Info("Checking %-v", repo)
}
total, orphaned, collected, deleted := int64(0), 0, 0, 0
if opts.Logger != nil {
defer func() {
if orphaned == 0 {
logger.Info("Found %d total LFSMetaObjects in %-v", total, repo)
} else if !autofix {
logger.Info("Found %d/%d orphaned LFSMetaObjects in %-v", orphaned, total, repo)
opts.Logger.Info("Found %d total LFSMetaObjects in %-v", total, repo)
} else if !opts.AutoFix {
opts.Logger.Info("Found %d/%d orphaned LFSMetaObjects in %-v", orphaned, total, repo)
} else {
logger.Info("Collected %d/%d orphaned/%d total LFSMetaObjects in %-v. %d removed from storage.", collected, orphaned, total, repo, deleted)
opts.Logger.Info("Collected %d/%d orphaned/%d total LFSMetaObjects in %-v. %d removed from storage.", collected, orphaned, total, repo, deleted)
}
}()
}
@ -60,17 +78,21 @@ func GarbageCollectLFSMetaObjectsForRepo(ctx context.Context, repo *repo_model.R
defer gitRepo.Close()
store := lfs.NewContentStore()
errStop := errors.New("STOPERR")
return git_model.IterateLFSMetaObjectsForRepo(ctx, repo.ID, func(ctx context.Context, metaObject *git_model.LFSMetaObject, count int64) error {
err = git_model.IterateLFSMetaObjectsForRepo(ctx, repo.ID, func(ctx context.Context, metaObject *git_model.LFSMetaObject, count int64) error {
if opts.NumberToCheckPerRepo > 0 && total > opts.NumberToCheckPerRepo {
return errStop
}
total++
pointerSha := git.ComputeBlobHash([]byte(metaObject.Pointer.StringContent()))
if gitRepo.IsObjectExist(pointerSha.String()) {
return nil
return git_model.MarkLFSMetaObject(ctx, metaObject.ID)
}
orphaned++
if !autofix {
if !opts.AutoFix {
return nil
}
// Non-existent pointer file
@ -100,6 +122,19 @@ func GarbageCollectLFSMetaObjectsForRepo(ctx context.Context, repo *repo_model.R
//
// It is likely that a week is potentially excessive but it should definitely be enough that any
// unassociated LFS object is genuinely unassociated.
OlderThan: time.Now().Add(-24 * 7 * time.Hour),
OlderThan: opts.OlderThan,
UpdatedLessRecentlyThan: opts.UpdatedLessRecentlyThan,
OrderByUpdated: true,
LoopFunctionAlwaysUpdates: true,
})
if err == errStop {
if opts.Logger != nil {
opts.Logger.Info("Processing stopped at %d total LFSMetaObjects in %-v", total, repo)
}
return nil
} else if err != nil {
return err
}
return nil
}