MongoDB整理物理空间碎片

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    接触过MySQL的同学应该知道，表进行批量的delete操作之后，数据盘空间并不会马上释放，innodb只是把删除的行对应的数据块做下标记，下次使用时候会优先使用。
    而MongoDB也有类似的情况，批量remove文档之后，磁盘空间并不会释放，我们可以使用compact进行碎片整理。
 

注意事项

• 实例的存储引擎为WiredTiger。
• 该操作会导致集合所属的数据库被锁定，且该数据库的读写操作将被阻塞，务必在业务低峰期操作。
   

单机或者副本集

查看集合基本信息

> db.usertable.stats().wiredTiger
{
    "metadata" : {
        "formatVersion" : 1
    },
    "creationString" : "access_pattern_hint=none,allocation_size=4KB,app_metadata=(formatVersion=1),assert=(commit_timestamp=none,durable_timestamp=none,read_timestamp=none),block_allocation=best,block_compressor=snappy,cache_resident=false,checksum=on,colgroups=,collator=,columns=,dictionary=0,encryption=(keyid=,name=),exclusive=false,extractor=,format=btree,huffman_key=,huffman_value=,ignore_in_memory_cache_size=false,immutable=false,internal_item_max=0,internal_key_max=0,internal_key_truncate=true,internal_page_max=4KB,key_format=q,key_gap=10,leaf_item_max=0,leaf_key_max=0,leaf_page_max=32KB,leaf_value_max=64MB,log=(enabled=true),lsm=(auto_throttle=true,bloom=true,bloom_bit_count=16,bloom_config=,bloom_hash_count=8,bloom_oldest=false,chunk_count_limit=0,chunk_max=5GB,chunk_size=10MB,merge_custom=(prefix=,start_generation=0,suffix=),merge_max=15,merge_min=0),memory_page_image_max=0,memory_page_max=10m,os_cache_dirty_max=0,os_cache_max=0,prefix_compression=false,prefix_compression_min=4,source=,split_deepen_min_child=0,split_deepen_per_child=0,split_pct=90,type=file,value_format=u",
    "type" : "file",
    "uri" : "statistics:table:ycsb1/collection-2--8436275121761636149",
    "LSM" : {
        "bloom filter false positives" : 0,
        "bloom filter hits" : 0,
        "bloom filter misses" : 0,
        "bloom filter pages evicted from cache" : 0,
        "bloom filter pages read into cache" : 0,
        "bloom filters in the LSM tree" : 0,
        "chunks in the LSM tree" : 0,
        "highest merge generation in the LSM tree" : 0,
        "queries that could have benefited from a Bloom filter that did not exist" : 0,
        "sleep for LSM checkpoint throttle" : 0,
        "sleep for LSM merge throttle" : 0,
        "total size of bloom filters" : 0
    },
    "block-manager" : {
        "allocations requiring file extension" : 49752,
        "blocks allocated" : 49774,
        "blocks freed" : 49761,
        "checkpoint size" : 0,
        "file allocation unit size" : 4096,
        "file bytes available for reuse" : 1420492800,
        "file magic number" : 120897,
        "file major version number" : 1,
        "file size in bytes" : 1420505088,
        "minor version number" : 0
    },
    "btree" : {
        "btree checkpoint generation" : 27,
        "btree clean tree checkpoint expiration time" : NumberLong("9223372036854775807"),
        "column-store fixed-size leaf pages" : 0,
        "column-store internal pages" : 0,
        "column-store variable-size RLE encoded values" : 0,
        "column-store variable-size deleted values" : 0,
        "column-store variable-size leaf pages" : 0,
        "fixed-record size" : 0,
        "maximum internal page key size" : 368,
        "maximum internal page size" : 4096,
        "maximum leaf page key size" : 2867,
        "maximum leaf page size" : 32768,
        "maximum leaf page value size" : 67108864,
        "maximum tree depth" : 4,
        "number of key/value pairs" : 0,
        "overflow pages" : 0,
        "pages rewritten by compaction" : 0,
        "row-store empty values" : 0,
        "row-store internal pages" : 0,
        "row-store leaf pages" : 0
    },
    "cache" : {
        "bytes currently in the cache" : 24555798,
        "bytes dirty in the cache cumulative" : 1563881912,
        "bytes read into cache" : 425821233,
        "bytes written from cache" : 1417712072,
        "checkpoint blocked page eviction" : 53,
        "data source pages selected for eviction unable to be evicted" : 81,
        "eviction walk passes of a file" : 2727,
        "eviction walk target pages histogram - 0-9" : 164,
        "eviction walk target pages histogram - 10-31" : 336,
        "eviction walk target pages histogram - 128 and higher" : 0,
        "eviction walk target pages histogram - 32-63" : 466,
        "eviction walk target pages histogram - 64-128" : 1761,
        "eviction walks abandoned" : 53,
        "eviction walks gave up because they restarted their walk twice" : 5,
        "eviction walks gave up because they saw too many pages and found no candidates" : 124,
        "eviction walks gave up because they saw too many pages and found too few candidates" : 60,
        "eviction walks reached end of tree" : 175,
        "eviction walks started from root of tree" : 243,
        "eviction walks started from saved location in tree" : 2484,
        "hazard pointer blocked page eviction" : 9,
        "in-memory page passed criteria to be split" : 356,
        "in-memory page splits" : 172,
        "internal pages evicted" : 404,
        "internal pages split during eviction" : 4,
        "leaf pages split during eviction" : 177,
        "modified pages evicted" : 48451,
        "overflow pages read into cache" : 0,
        "page split during eviction deepened the tree" : 1,
        "page written requiring cache overflow records" : 0,
        "pages read into cache" : 14676,
        "pages read into cache after truncate" : 1,
        "pages read into cache after truncate in prepare state" : 0,
        "pages read into cache requiring cache overflow entries" : 0,
        "pages requested from the cache" : 7689354,
        "pages seen by eviction walk" : 1194026,
        "pages written from cache" : 49765,
        "pages written requiring in-memory restoration" : 2,
        "tracked dirty bytes in the cache" : 0,
        "unmodified pages evicted" : 14256
    },
    "cache_walk" : {
        "Average difference between current eviction generation when the page was last considered" : 0,
        "Average on-disk page image size seen" : 0,
        "Average time in cache for pages that have been visited by the eviction server" : 0,
        "Average time in cache for pages that have not been visited by the eviction server" : 0,
        "Clean pages currently in cache" : 0,
        "Current eviction generation" : 0,
        "Dirty pages currently in cache" : 0,
        "Entries in the root page" : 0,
        "Internal pages currently in cache" : 0,
        "Leaf pages currently in cache" : 0,
        "Maximum difference between current eviction generation when the page was last considered" : 0,
        "Maximum page size seen" : 0,
        "Minimum on-disk page image size seen" : 0,
        "Number of pages never visited by eviction server" : 0,
        "On-disk page image sizes smaller than a single allocation unit" : 0,
        "Pages created in memory and never written" : 0,
        "Pages currently queued for eviction" : 0,
        "Pages that could not be queued for eviction" : 0,
        "Refs skipped during cache traversal" : 0,
        "Size of the root page" : 0,
        "Total number of pages currently in cache" : 0
    },
    "compression" : {
        "compressed page maximum internal page size prior to compression" : 4096,
        "compressed page maximum leaf page size prior to compression " : 32768,
        "compressed pages read" : 88,
        "compressed pages written" : 105,
        "page written failed to compress" : 49176,
        "page written was too small to compress" : 484
    },
    "cursor" : {
        "bulk loaded cursor insert calls" : 0,
        "cache cursors reuse count" : 981,
        "close calls that result in cache" : 0,
        "create calls" : 5,
        "insert calls" : 982334,
        "insert key and value bytes" : 1399137825,
        "modify" : 0,
        "modify key and value bytes affected" : 0,
        "modify value bytes modified" : 0,
        "next calls" : 990110,
        "open cursor count" : 0,
        "operation restarted" : 0,
        "prev calls" : 2,
        "remove calls" : 982334,
        "remove key bytes removed" : 3846971,
        "reserve calls" : 0,
        "reset calls" : 2971484,
        "search calls" : 1964668,
        "search near calls" : 990109,
        "truncate calls" : 0,
        "update calls" : 0,
        "update key and value bytes" : 0,
        "update value size change" : 0
    },
    "reconciliation" : {
        "dictionary matches" : 0,
        "fast-path pages deleted" : 0,
        "internal page key bytes discarded using suffix compression" : 99217,
        "internal page multi-block writes" : 9,
        "internal-page overflow keys" : 0,
        "leaf page key bytes discarded using prefix compression" : 0,
        "leaf page multi-block writes" : 179,
        "leaf-page overflow keys" : 0,
        "maximum blocks required for a page" : 1,
        "overflow values written" : 0,
        "page checksum matches" : 413,
        "page reconciliation calls" : 50044,
        "page reconciliation calls for eviction" : 47098,
        "pages deleted" : 49020
    },
    "session" : {
        "object compaction" : 0
    },
    "transaction" : {
        "update conflicts" : 0
    }
}

删除文档

> use ycsb1
switched to db ycsb1
> 
> db.usertable.remove({})
WriteResult({ "nRemoved" : 982334 })
> db.usertable.count()
0

可以看到集合已经清空。

查看磁盘占用

找到数据目录

[root@mongodb data]# du -sm ycsb1/
1405    ycsb1/

碎片整理

> db.runCommand({compact:"usertable",force:true})
{ "ok" : 1 }

查看磁盘占用

[root@mongodb data]# du -sm ycsb1/
1   ycsb1/

可以看到磁盘空间已经释放。
接下来登录secondary节点进行同样的操作。
 

分片集

查看分片信息

mongos> sh.status()
--- Sharding Status --- 
  sharding version: {
    "_id" : 1,
    "minCompatibleVersion" : 5,
    "currentVersion" : 6,
    "clusterId" : ObjectId("60545017224c766911a9c440")
  }
  shards:
        {  "_id" : "hdshard1",  "host" : "hdshard1/172.16.254.136:40001,172.16.254.137:40001,172.16.254.138:40001",  "state" : 1 }
        {  "_id" : "hdshard2",  "host" : "hdshard2/172.16.254.136:40002,172.16.254.137:40002,172.16.254.138:40002",  "state" : 1 }
        {  "_id" : "hdshard3",  "host" : "hdshard3/172.16.254.136:40003,172.16.254.137:40003,172.16.254.138:40003",  "state" : 1 }
  active mongoses:
        "4.2.12" : 3
  autosplit:
        Currently enabled: yes
  balancer:
        Currently enabled:  yes
        Currently running:  no
        Failed balancer rounds in last 5 attempts:  0
        Migration Results for the last 24 hours: 
                52 : Success
  databases:
        {  "_id" : "config",  "primary" : "config",  "partitioned" : true }
                config.system.sessions
                        shard key: { "_id" : 1 }
                        unique: false
                        balancing: true
                        chunks:
                                hdshard1    342
                                hdshard2    341
                                hdshard3    341
                        too many chunks to print, use verbose if you want to force print
        {  "_id" : "db1",  "primary" : "hdshard3",  "partitioned" : true,  "version" : {  "uuid" : UUID("71bb472c-7896-4a31-a77c-e3aaf723be3c"),  "lastMod" : 1 } }
        {  "_id" : "db2",  "primary" : "hdshard2",  "partitioned" : false,  "version" : {  "uuid" : UUID("add90941-a8b1-4c40-94e9-9ccc38d73096"),  "lastMod" : 2 } }
        {  "_id" : "db3",  "primary" : "hdshard3",  "partitioned" : false,  "version" : {  "uuid" : UUID("f0278f73-d999-453f-8739-eac30a8bcf9b"),  "lastMod" : 1 } }
        {  "_id" : "recommend",  "primary" : "hdshard1",  "partitioned" : true,  "version" : {  "uuid" : UUID("cb833b8e-cc4f-4c52-83c3-719aa383bac4"),  "lastMod" : 1 } }
                recommend.rcmd_1_min_tag_mei_rong
                        shard key: { "_id" : "hashed" }
                        unique: false
                        balancing: true
                        chunks:
                                hdshard1    2
                                hdshard2    3
                                hdshard3    3
                        { "_id" : { "$minKey" : 1 } } -->> { "_id" : NumberLong("-6701866976688134138") } on : hdshard3 Timestamp(9, 0) 
                        { "_id" : NumberLong("-6701866976688134138") } -->> { "_id" : NumberLong("-4163240026901542572") } on : hdshard3 Timestamp(3, 0) 
                        { "_id" : NumberLong("-4163240026901542572") } -->> { "_id" : NumberLong("-1616330844721205691") } on : hdshard2 Timestamp(7, 1) 
                        { "_id" : NumberLong("-1616330844721205691") } -->> { "_id" : NumberLong("909129560750995399") } on : hdshard3 Timestamp(5, 0) 
                        { "_id" : NumberLong("909129560750995399") } -->> { "_id" : NumberLong("3449289120186727718") } on : hdshard2 Timestamp(6, 0) 
                        { "_id" : NumberLong("3449289120186727718") } -->> { "_id" : NumberLong("5980358241733552715") } on : hdshard2 Timestamp(10, 0) 
                        { "_id" : NumberLong("5980358241733552715") } -->> { "_id" : NumberLong("8520801504243263436") } on : hdshard1 Timestamp(8, 1) 
                        { "_id" : NumberLong("8520801504243263436") } -->> { "_id" : { "$maxKey" : 1 } } on : hdshard1 Timestamp(1, 7) 
                recommend.rcmd_1_tag_li_liao
                        shard key: { "_id" : 1 }
                        unique: false
                        balancing: true
                        chunks:
                                hdshard1    36
                                hdshard2    35
                                hdshard3    36
                        too many chunks to print, use verbose if you want to force print
        {  "_id" : "ycsb",  "primary" : "hdshard2",  "partitioned" : true,  "version" : {  "uuid" : UUID("df4f702f-bb9f-477c-a327-c4b4f28ccf8f"),  "lastMod" : 1 } }
                ycsb.usertable
                        shard key: { "_id" : "hashed" }
                        unique: false
                        balancing: true
                        chunks:
                                hdshard1    11
                                hdshard2    11
                                hdshard3    11
                        too many chunks to print, use verbose if you want to force print
        {  "_id" : "ycsb1",  "primary" : "hdshard2",  "partitioned" : true,  "version" : {  "uuid" : UUID("c7e227d8-0739-41c7-b47e-9d36065454d3"),  "lastMod" : 1 } }
                ycsb1.usertable
                        shard key: { "_id" : "hashed" }
                        unique: false
                        balancing: true
                        chunks:
                                hdshard1    8
                                hdshard2    8
                                hdshard3    9
                        too many chunks to print, use verbose if you want to force print

可以看到ycsb1库的主分片节点是hdshard2。

删除文档

mongos> use ycsb1
switched to db ycsb1
mongos> show collections
usertable
mongos> db.usertable.remove({})
WriteResult({ "nRemoved" : 982334 })
mongos> db.usertable.count()
0

查看磁盘

登录分片所在服务器，进入数据目录

[mongodb@mongo7 shard2]$ du -sm ycsb1
1448    ycsb1

碎片整理

hdshard2:PRIMARY> db.runCommand({compact:"usertable",force:true})
{
    "ok" : 1,
    "$gleStats" : {
        "lastOpTime" : Timestamp(0, 0),
        "electionId" : ObjectId("7fffffff0000000000000030")
    },
    "lastCommittedOpTime" : Timestamp(1619505175, 4),
    "$configServerState" : {
        "opTime" : {
            "ts" : Timestamp(1619505181, 1),
            "t" : NumberLong(22)
        }
    },
    "$clusterTime" : {
        "clusterTime" : Timestamp(1619505181, 1),
        "signature" : {
            "hash" : BinData(0,"zcROSPOVYMxzJouTvGAZ4S0Ddh4="),
            "keyId" : NumberLong("6941260985399246879")
        }
    },
    "operationTime" : Timestamp(1619505175, 4)
}

查看磁盘

[mongodb@mongo7 shard2]$ du -sm ycsb1
1   ycsb1

可以看到磁盘空间已经释放。
接下来登录secondary节点重复上述操作。
 

说明

• 如果新数据写入较快，可以不进行compact，这些碎片会很快被使用。
• 如果使用db.collection.drop()进行集合删除，无需进行碎片整理。
• 如果涉及副本集，需在primary节点和secondary节点进行同样的操作，compact不会传递给secondary节点。

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