store, compact, bucket: Delay deletes by scheduling block deletion wi…

…th deletion-mark.json file (#2136)

Signed-off-by: khyatisoneji <[email protected]>

CHANGELOG.md

@@ -23,6 +23,9 @@ We use *breaking* word for marking changes that are not backward compatible (rel
 
 ### Changed
 
+- [#2136](https://github.com/thanos-io/thanos/pull/2136) store, compact, bucket: schedule block deletion by adding deletion-mark.json. This adds a consistent way for multiple readers and writers to access object storage.
+Since there are no consistency guarantees provided by some Object Storage providers, this PR adds a consistent lock-free way of dealing with Object Storage irrespective of the choice of object storage. In order to achieve this co-ordination, blocks are not deleted directly. Instead, blocks are marked for deletion by uploading `deletion-mark.json` file for the block that was chosen to be deleted. This file contains unix time of when the block was marked for deletion.
+
 - [#2090](https://github.com/thanos-io/thanos/issues/2090) *breaking* Downsample command: the `downsample` command has moved as the `thanos bucket` sub-command, and cannot be called via `thanos downsample` any more.
 
 ## [v0.11.0](https://github.com/thanos-io/thanos/releases/tag/v0.11.0) - 2020.03.02

cmd/thanos/bucket.go

@@ -85,6 +85,12 @@ func registerBucketVerify(m map[string]setupFunc, root *kingpin.CmdClause, name
 		Short('i').Default(verifier.IndexIssueID, verifier.OverlappedBlocksIssueID).Strings()
 	idWhitelist := cmd.Flag("id-whitelist", "Block IDs to verify (and optionally repair) only. "+
 		"If none is specified, all blocks will be verified. Repeated field").Strings()
+	deleteDelay := modelDuration(cmd.Flag("delete-delay", "Duration after which blocks marked for deletion would be deleted permanently from source bucket by compactor component. "+
+		"If delete-delay is non zero, blocks will be marked for deletion and compactor component is required to delete blocks from source bucket. "+
+		"If delete-delay is 0, blocks will be deleted straight away. Use this if you want to get rid of or move the block immediately. "+
+		"Note that deleting blocks immediately can cause query failures, if store gateway still has the block loaded, "+
+		"or compactor is ignoring the deletion because it's compacting the block at the same time.").
+		Default("0s"))
 	m[name+" verify"] = func(g *run.Group, logger log.Logger, reg *prometheus.Registry, _ opentracing.Tracer, _ <-chan struct{}, _ bool) error {
 		confContentYaml, err := objStoreConfig.Content()
 		if err != nil {
@@ -140,9 +146,9 @@ func registerBucketVerify(m map[string]setupFunc, root *kingpin.CmdClause, name
 		}
 
 		if *repair {
-			v = verifier.NewWithRepair(logger, bkt, backupBkt, fetcher, issues)
+			v = verifier.NewWithRepair(logger, reg, bkt, backupBkt, fetcher, time.Duration(*deleteDelay), issues)
 		} else {
-			v = verifier.New(logger, bkt, fetcher, issues)
+			v = verifier.New(logger, reg, bkt, fetcher, time.Duration(*deleteDelay), issues)
 		}
 
 		var idMatcher func(ulid.ULID) bool = nil

cmd/thanos/compact.go

@@ -126,6 +126,13 @@ func registerCompact(m map[string]setupFunc, app *kingpin.Application) {
 	compactionConcurrency := cmd.Flag("compact.concurrency", "Number of goroutines to use when compacting groups.").
 		Default("1").Int()
 
+	deleteDelay := modelDuration(cmd.Flag("delete-delay", "Time before a block marked for deletion is deleted from bucket. "+
+		"If delete-delay is non zero, blocks will be marked for deletion and compactor component will delete blocks marked for deletion from the bucket. "+
+		"If delete-delay is 0, blocks will be deleted straight away. "+
+		"Note that deleting blocks immediately can cause query failures, if store gateway still has the block loaded, "+
+		"or compactor is ignoring the deletion because it's compacting the block at the same time.").
+		Default("48h"))
+
 	selectorRelabelConf := regSelectorRelabelFlags(cmd)
 
 	m[component.Compact.String()] = func(g *run.Group, logger log.Logger, reg *prometheus.Registry, tracer opentracing.Tracer, _ <-chan struct{}, _ bool) error {
@@ -135,6 +142,7 @@ func registerCompact(m map[string]setupFunc, app *kingpin.Application) {
 			*dataDir,
 			objStoreConfig,
 			time.Duration(*consistencyDelay),
+			time.Duration(*deleteDelay),
 			*haltOnError,
 			*acceptMalformedIndex,
 			*wait,
@@ -164,6 +172,7 @@ func runCompact(
 	dataDir string,
 	objStoreConfig *extflag.PathOrContent,
 	consistencyDelay time.Duration,
+	deleteDelay time.Duration,
 	haltOnError bool,
 	acceptMalformedIndex bool,
 	wait bool,
@@ -194,6 +203,25 @@ func runCompact(
 		Name: "thanos_compactor_aborted_partial_uploads_deletion_attempts_total",
 		Help: "Total number of started deletions of blocks that are assumed aborted and only partially uploaded.",
 	})
+	blocksCleaned := promauto.With(reg).NewCounter(prometheus.CounterOpts{
+		Name: "thanos_compactor_blocks_cleaned_total",
+		Help: "Total number of blocks deleted in compactor.",
+	})
+	blockCleanupFailures := promauto.With(reg).NewCounter(prometheus.CounterOpts{
+		Name: "thanos_compactor_block_cleanup_failures_total",
+		Help: "Failures encountered while deleting blocks in compactor.",
+	})
+	blocksMarkedForDeletion := promauto.With(reg).NewCounter(prometheus.CounterOpts{
+		Name: "thanos_compactor_blocks_marked_for_deletion_total",
+		Help: "Total number of blocks marked for deletion in compactor.",
+	})
+	_ = promauto.With(reg).NewGaugeFunc(prometheus.GaugeOpts{
+		Name: "thanos_delete_delay_seconds",
+		Help: "Configured delete delay in seconds.",
+	}, func() float64 {
+		return deleteDelay.Seconds()
+	})
+
 	downsampleMetrics := newDownsampleMetrics(reg)
 
 	httpProbe := prober.NewHTTP()
@@ -245,18 +273,22 @@ func runCompact(
 		}
 	}()
 
+	// While fetching blocks, we filter out blocks that were marked for deletion by using IgnoreDeletionMarkFilter.
+	// The delay of  deleteDelay/2 is added to ensure we fetch blocks that are meant to be deleted but do not have a replacement yet.
+	ignoreDeletionMarkFilter := block.NewIgnoreDeletionMarkFilter(logger, bkt, time.Duration(deleteDelay.Seconds()/2)*time.Second)
 	duplicateBlocksFilter := block.NewDeduplicateFilter()
 	prometheusRegisterer := extprom.WrapRegistererWithPrefix("thanos_", reg)
 	metaFetcher, err := block.NewMetaFetcher(logger, 32, bkt, "", prometheusRegisterer,
 		block.NewLabelShardedMetaFilter(relabelConfig).Filter,
 		block.NewConsistencyDelayMetaFilter(logger, consistencyDelay, prometheusRegisterer).Filter,
+		ignoreDeletionMarkFilter.Filter,
 		duplicateBlocksFilter.Filter,
 	)
 	if err != nil {
 		return errors.Wrap(err, "create meta fetcher")
 	}
 
-	sy, err := compact.NewSyncer(logger, reg, bkt, metaFetcher, duplicateBlocksFilter, blockSyncConcurrency, acceptMalformedIndex, false)
+	sy, err := compact.NewSyncer(logger, reg, bkt, metaFetcher, duplicateBlocksFilter, ignoreDeletionMarkFilter, blocksMarkedForDeletion, blockSyncConcurrency, acceptMalformedIndex, false)
 	if err != nil {
 		return errors.Wrap(err, "create syncer")
 	}
@@ -290,6 +322,7 @@ func runCompact(
 		return errors.Wrap(err, "clean working downsample directory")
 	}
 
+	blocksCleaner := compact.NewBlocksCleaner(logger, bkt, ignoreDeletionMarkFilter, deleteDelay, blocksCleaned, blockCleanupFailures)
 	compactor, err := compact.NewBucketCompactor(logger, sy, comp, compactDir, bkt, concurrency)
 	if err != nil {
 		cancel()
@@ -331,11 +364,15 @@ func runCompact(
 			level.Warn(logger).Log("msg", "downsampling was explicitly disabled")
 		}
 
-		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, metaFetcher, retentionByResolution); err != nil {
+		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, metaFetcher, retentionByResolution, blocksMarkedForDeletion); err != nil {
 			return errors.Wrap(err, fmt.Sprintf("retention failed"))
 		}
 
-		compact.BestEffortCleanAbortedPartialUploads(ctx, logger, metaFetcher, bkt, partialUploadDeleteAttempts)
+		if err := blocksCleaner.DeleteMarkedBlocks(ctx); err != nil {
+			return errors.Wrap(err, "error cleaning blocks")
+		}
+
+		compact.BestEffortCleanAbortedPartialUploads(ctx, logger, metaFetcher, bkt, partialUploadDeleteAttempts, blocksMarkedForDeletion)
 		return nil
 	}
 

cmd/thanos/store.go

@@ -84,6 +84,13 @@ func registerStore(m map[string]setupFunc, app *kingpin.Application) {
 	consistencyDelay := modelDuration(cmd.Flag("consistency-delay", "Minimum age of all blocks before they are being read. Set it to safe value (e.g 30m) if your object storage is eventually consistent. GCS and S3 are (roughly) strongly consistent.").
 		Default("0s"))
 
+	ignoreDeletionMarksDelay := modelDuration(cmd.Flag("ignore-deletion-marks-delay", "Duration after which the blocks marked for deletion will be filtered out while fetching blocks. "+
+		"The idea of ignore-deletion-marks-delay is to ignore blocks that are marked for deletion with some delay. This ensures store can still serve blocks that are meant to be deleted but do not have a replacement yet. "+
+		"If delete-delay duration is provided to compactor or bucket verify component, it will upload deletion-mark.json file to mark after what duration the block should be deleted rather than deleting the block straight away. "+
+		"If delete-delay is non-zero for compactor or bucket verify component, ignore-deletion-marks-delay should be set to (delete-delay)/2 so that blocks marked for deletion are filtered out while fetching blocks before being deleted from bucket. "+
+		"Default is 24h, half of the default value for --delete-delay on compactor.").
+		Default("24h"))
+
 	m[component.Store.String()] = func(g *run.Group, logger log.Logger, reg *prometheus.Registry, tracer opentracing.Tracer, _ <-chan struct{}, debugLogging bool) error {
 		if minTime.PrometheusTimestamp() > maxTime.PrometheusTimestamp() {
 			return errors.Errorf("invalid argument: --min-time '%s' can't be greater than --max-time '%s'",
@@ -120,6 +127,7 @@ func registerStore(m map[string]setupFunc, app *kingpin.Application) {
 			*advertiseCompatibilityLabel,
 			*enableIndexHeader,
 			time.Duration(*consistencyDelay),
+			time.Duration(*ignoreDeletionMarksDelay),
 		)
 	}
 }
@@ -153,6 +161,7 @@ func runStore(
 	advertiseCompatibilityLabel bool,
 	enableIndexHeader bool,
 	consistencyDelay time.Duration,
+	ignoreDeletionMarksDelay time.Duration,
 ) error {
 	grpcProbe := prober.NewGRPC()
 	httpProbe := prober.NewHTTP()
@@ -225,11 +234,13 @@ func runStore(
 		return errors.Wrap(err, "create index cache")
 	}
 
+	ignoreDeletionMarkFilter := block.NewIgnoreDeletionMarkFilter(logger, bkt, ignoreDeletionMarksDelay)
 	prometheusRegisterer := extprom.WrapRegistererWithPrefix("thanos_", reg)
 	metaFetcher, err := block.NewMetaFetcher(logger, fetcherConcurrency, bkt, dataDir, prometheusRegisterer,
 		block.NewTimePartitionMetaFilter(filterConf.MinTime, filterConf.MaxTime).Filter,
 		block.NewLabelShardedMetaFilter(relabelConfig).Filter,
 		block.NewConsistencyDelayMetaFilter(logger, consistencyDelay, prometheusRegisterer).Filter,
+		ignoreDeletionMarkFilter.Filter,
 		block.NewDeduplicateFilter().Filter,
 	)
 	if err != nil {

docs/components/bucket.md

@@ -26,11 +26,12 @@ config:
 Bucket can be extended to add more subcommands that will be helpful when working with object storage buckets
 by adding a new command within `/cmd/thanos/bucket.go`.
 
-
 ## Deployment
+
 ## Flags
 
-[embedmd]:# (flags/bucket.txt $)
+[embedmd]: # "flags/bucket.txt $"
+
 ```$
 usage: thanos bucket [<flags>] <command> [<args> ...]
 
@@ -98,7 +99,8 @@ Example:
 $ thanos bucket web --objstore.config-file="..."
 ```
 
-[embedmd]:# (flags/bucket_web.txt)
+[embedmd]: # "flags/bucket_web.txt"
+
 ```txt
 usage: thanos bucket web [<flags>]
 
@@ -170,7 +172,8 @@ Example:
 $ thanos bucket verify --objstore.config-file="..."
 ```
 
-[embedmd]:# (flags/bucket_verify.txt)
+[embedmd]: # "flags/bucket_verify.txt"
+
 ```txt
 usage: thanos bucket verify [<flags>]
 
@@ -222,7 +225,11 @@ Flags:
                            Block IDs to verify (and optionally repair) only. If
                            none is specified, all blocks will be verified.
                            Repeated field
-
+  --delete-delay=0s        Duration after which blocks marked for deletion would be deleted permanently from source bucket by compactor component.
+                           If delete-delay is non zero, blocks will be marked for deletion and compactor component is required to delete blocks from source bucket.
+                           If delete-delay is 0, blocks will be deleted straight away. Use this if you want to get rid of or move the block immediately.
+                           Note that deleting blocks immediately can cause query failures, if store gateway still has the block
+                           loaded, or compactor is ignoring the deletion because it's compacting the block at the same time.
 ```
 
 ### ls
@@ -235,7 +242,8 @@ Example:
 $ thanos bucket ls -o json --objstore.config-file="..."
 ```
 
-[embedmd]:# (flags/bucket_ls.txt)
+[embedmd]: # "flags/bucket_ls.txt"
+
 ```txt
 usage: thanos bucket ls [<flags>]
 
@@ -276,11 +284,13 @@ Flags:
 `bucket inspect` is used to inspect buckets in a detailed way using stdout in ASCII table format.
 
 Example:
+
 ```
 $ thanos bucket inspect -l environment=\"prod\" --objstore.config-file="..."
 ```
 
-[embedmd]:# (flags/bucket_inspect.txt)
+[embedmd]: # "flags/bucket_inspect.txt"
+
 ```txt
 usage: thanos bucket inspect [<flags>]
 

docs/components/compact.md

@@ -11,8 +11,8 @@ It is generally not semantically concurrency safe and must be deployed as a sing
 
 It is also responsible for downsampling of data:
 
-* creating 5m downsampling for blocks larger than **40 hours** (2d, 2w)
-* creating 1h downsampling for blocks larger than **10 days** (2w).
+- creating 5m downsampling for blocks larger than **40 hours** (2d, 2w)
+- creating 1h downsampling for blocks larger than **10 days** (2w).
 
 Example:
 
@@ -35,9 +35,9 @@ On-disk data is safe to delete between restarts and should be the first attempt
 
 Resolution - distance between data points on your graphs. E.g.
 
-* raw - the same as scrape interval at the moment of data ingestion
-* 5m - data point is every 5 minutes
-* 1h - data point is every 1h
+- raw - the same as scrape interval at the moment of data ingestion
+- 5m - data point is every 5 minutes
+- 1h - data point is every 1h
 
 Keep in mind, that the initial goal of downsampling is not saving disk space (Read further for elaboration on storage space consumption). The goal of downsampling is providing an opportunity to get fast results for range queries of big time intervals like months or years. In other words, if you set `--retention.resolution-raw` less then `--retention.resolution-5m` and `--retention.resolution-1h` - you might run into a problem of not being able to "zoom in" to your historical data.
 
@@ -64,9 +64,18 @@ your Prometheus instances, so that the compactor will be able to group blocks by
 By _persistent_, we mean that one Prometheus instance must keep the same labels if it restarts, so that the compactor will keep
 compacting blocks from an instance even when a Prometheus instance goes down for some time.
 
+## Block Deletion
+
+Depending on the Object Storage provider like S3, GCS, Ceph etc; we can divide the storages into strongly consistent or eventually consistent.
+Since there are no consistency guarantees provided by some Object Storage providers, we have to make sure that we have a consistent lock-free way of dealing with Object Storage irrespective of the choice of object storage.
+
+In order to achieve this co-ordination, blocks are not deleted directly. Instead, blocks are marked for deletion by uploading
+`deletion-mark.json` file for the block that was chosen to be deleted. This file contains unix time of when the block was marked for deletion.
+
 ## Flags
 
-[embedmd]:# (flags/compact.txt $)
+[embedmd]: # "flags/compact.txt $"
+
 ```$
 usage: thanos compact [<flags>]
 
@@ -146,5 +155,10 @@ Flags:
                                selecting blocks. It follows native Prometheus
                                relabel-config syntax. See format details:
                                https://prometheus.io/docs/prometheus/latest/configuration/configuration/#relabel_config
-
+      --delete-delay=48h       Time before a block marked for deletion is deleted from bucket.
+		                           If delete-delay is non zero, blocks will be marked for deletion and compactor component will delete blocks marked for deletion from the bucket.
+		                           If delete-delay is 0, blocks will be deleted straight away.
+                               Use this if you want to get rid of or move the block immediately.
+		                           Note that deleting blocks immediately can cause query failures, if store gateway still has the block
+                               loaded, or compactor is ignoring the deletion because it's compacting the block at the same time.
 ```

docs/components/store.md

@@ -139,7 +139,10 @@ Flags:
                                  details:
                                  https://prometheus.io/docs/prometheus/latest/configuration/configuration/#relabel_config
       --consistency-delay=30m    Minimum age of all blocks before they are being read.
-
+      --ignore-deletion-marks-delay=24h
+                                 Duration after which the blocks marked for deletion will be filtered out while fetching blocks.
+                                 The idea of ignore-deletion-marks-delay is to ignore blocks that are marked for deletion with some delay. This ensures store can still serve blocks that are meant to be deleted but do not have a replacement yet. If delete-delay duration is provided to compactor or bucket verify component, it will upload deletion-mark.json file to mark after what duration the block should be deleted rather than deleting the block straight away.
+		                             If delete-delay is non-zero for compactor or bucket verify component, ignore-deletion-marks-delay should be set to (delete-delay)/2 so that blocks marked for deletion are filtered out while fetching blocks before being deleted from bucket. Default is 24h, half of the default value for --delete-delay on compactor.
 ```
 
 ## Time based partitioning

docs/proposals/201901-read-write-operations-bucket.md

@@ -2,7 +2,7 @@
 title: Read-Write coordination free operational contract for object storage
 type: proposal
 menu: proposals
-status: accepted
+status: complete
 owner: bwplotka
 ---
 
@@ -179,7 +179,7 @@ We schedule deletions instead of doing them straight away for 3 reasons:
 * In further delete steps, starting with meta.json first ensures integrity mark being deleted first, so in case of deletion process being stopped, we can treat this block as partial block (rule 4th) and delete it gracefully.
 
 Along with this, we also store information about when the block was scheduled to be deleted so that it can be deleted at a later point in time.
-To do so, we create a file `compactor-meta.json` where we store information about when the block was scheduled to be deleted.
+To do so, we create a file `deletion-mark.json` where we store information about when the block was scheduled to be deleted.
 Storing the information in a file makes it resilient to failures that result in restarts.
 
 There might be exception for malformed blocks that blocks compaction or reader operations. Since we may need to unblock the system
@@ -189,7 +189,7 @@ immediately the block can be forcibly removed meaning that query failures may oc
 
 This is to make sure we don't forcibly remove block which is still loaded on reader side.
 
-We check the `compactor-meta.json` file to identify if the block has to be deleted. After 15 minutes of marking the block to be deleted, we are ok to delete the whole block directory.
+We check the `deletion-mark.json` file to identify if the block has to be deleted. After 15 minutes of marking the block to be deleted, we are ok to delete the whole block directory.
 
 ## Risks