[SERVER-18836] diskspace usage Created: 05/Jun/15  Updated: 01/Jul/15  Resolved: 01/Jul/15

Status: Closed
Project: Core Server
Component/s: Admin, WiredTiger
Affects Version/s: None
Fix Version/s: None

Type: Bug Priority: Major - P3
Reporter: Patrick Lauber Assignee: Ramon Fernandez Marina
Resolution: Incomplete Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Operating System: ALL
Participants:

 Description   

I have a db with 30m entries that get touched 6-20 times and fields added to the docs. WiredTiger is used. After import the discspace needed is 5GB. After i add fields to the docs the diskspace usage is 30GB. Compact and repairDatabase do not reduce the diskspace. If i add a new secondary it uses about 6GB of diskspace after sync. So a usage of 5 times the diskspace is not acceptable. Also the diskspace used is bigger then the uncompressed data size.



 Comments   
Comment by Ramon Fernandez Marina [ 01/Jul/15 ]

digi604, we haven't heard back from you for a while so I'm going to close this ticket. If this is still an issue for you please send us the information requested above (output of ls -laR on the dbpath of both the primary (using more space) and a secondary using less space) and we'll reopen this ticket for further investigation.

Thanks,
Ramón.

Comment by Ramon Fernandez Marina [ 15/Jun/15 ]

digi604, if we could see the output of ls -laR on the dbpath of both your primary (which uses more space) and a secondary (using less space) that may help us understand what's going on.

Thanks,
Ramón.

Comment by Patrick Lauber [ 09/Jun/15 ]

1. 3.0.3
2. cluster via mms with 3 shards, 2 nodes per replica set on AWS
3. i see the increase in diskspace on all nodes... except the one i added after.
4. sample doc:

 "_id" : ObjectId("555b41b841480f5fb09ec96f"), "week_of_year" : "CW51", "event_type" : "uiReady", "timestamp" : ISODate("2013-12-23T08:55:56.008Z"), "event_year" : 2013, "lat" : "41.511324033063005", "session_id" : "1387788953982", "device" : "000-00000000-2267-1134-0000-0000138ae38a", "_lock_expire" : ISODate("2015-05-19T13:59:20.754Z"), "quarter" : "Q4", "app_type" : "android", "_last_modified" : ISODate("2015-05-19T13:59:20.754Z"), "lon" : "27.281794485318883", "day_of_month" : 23, "_lock_id" : 0, "params" : "", "event_day" : "Monday", "month_of_year" : 12, "event_extra" : "GT-N8005", "_created" : ISODate("2013-12-23T11:04:51Z"), "_status" : "new", "app_version" : 10, "event_month" : "December", "app_slug" : "achilles_admin", "geo:tag" : { "country_iso_code" : "TR", "area_name" : "Kırklareli", "full_address" : "Unnamed Road, Kırklareli, Turkey", "street" : "Unnamed Road", "area_iso_code" : "Kırklareli", "country_name" : "Turkey" }, "rep_name" : "503357", "event_name" : "", "licence_id" : 240, "app_name" : "Aİ Achilles", "app_id" : null }

stats:

b.all_events.stats()
{
	"sharded" : true,
	"capped" : false,
	"ns" : "events.all_events",
	"count" : 82055375,
	"size" : 79085587355,
	"storageSize" : 83525902336,
	"totalIndexSize" : 13443317760,
	"indexSizes" : {
		"_id_" : 1330913280,
		"_id_hashed" : 2883305472,
		"app_name_1" : 368902144,
		"app_slug_1" : 300875776,
		"event_day_1" : 294694912,
		"event_name_1" : 314699776,
		"event_type_1" : 431022080,
		"geo:ip_1" : 414355456,
		"geo:ip_1_ip_1" : 408981504,
		"geo:tag_1" : 1102467072,
		"geo:tag_1_lat_1" : 1538174976,
		"lat_1" : 684998656,
		"rep_name_1" : 385871872,
		"session_id_-1" : 872226816,
		"session_id_1" : 853561344,
		"timestamp_-1" : 1258266624
	},
	"avgObjSize" : 963.8075184593331,
	"nindexes" : 16,
	"nchunks" : 1505,
	"shards" : {
		"eventsdata_0" : {
			"ns" : "events.all_events",
			"count" : 28052515,
			"size" : 27040369714,
			"avgObjSize" : 963,
			"storageSize" : 30186409984,
			"capped" : false,
			"wiredTiger" : {
				"metadata" : {
					"formatVersion" : 1
				},
				"creationString" : "allocation_size=4KB,app_metadata=(formatVersion=1),block_allocation=best,block_compressor=snappy,cache_resident=0,checkpoint=(WiredTigerCheckpoint.15686=(addr=\"01e37053ac81e45baa060ee37053ad8ae43f693093e37053b789e4a34a0577808080e507073fefc0e5070945dfc0\",order=15686,time=1433843249,size=30220353536,write_gen=47867019)),checkpoint_lsn=(1640,14751232),checksum=on,collator=,columns=,dictionary=0,format=btree,huffman_key=,huffman_value=,id=58,internal_item_max=0,internal_key_max=0,internal_key_truncate=,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=1MB,memory_page_max=10m,os_cache_dirty_max=0,os_cache_max=0,prefix_compression=0,prefix_compression_min=4,split_deepen_min_child=0,split_deepen_per_child=0,split_pct=90,value_format=u,version=(major=1,minor=1)",
				"type" : "file",
				"uri" : "statistics:table:collection-55--7239878682253991957",
				"LSM" : {
					"bloom filters in the LSM tree" : 0,
					"bloom filter false positives" : 0,
					"bloom filter hits" : 0,
					"bloom filter misses" : 0,
					"bloom filter pages evicted from cache" : 0,
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					"total size of bloom filters" : 0,
					"sleep for LSM checkpoint throttle" : 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 merge throttle" : 0
				},
				"block-manager" : {
					"file allocation unit size" : 4096,
					"blocks allocated" : 22233566,
					"checkpoint size" : 30220353536,
					"allocations requiring file extension" : 2033163,
					"blocks freed" : 19650184,
					"file magic number" : 120897,
					"file major version number" : 1,
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					"file bytes available for reuse" : 30216192,
					"file size in bytes" : 30186409984
				},
				"btree" : {
					"btree checkpoint generation" : 15212,
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					"column-store internal pages" : 0,
					"column-store variable-size leaf pages" : 0,
					"pages rewritten by compaction" : 0,
					"number of key/value pairs" : 0,
					"fixed-record size" : 0,
					"maximum tree depth" : 9,
					"maximum internal page key size" : 368,
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					"maximum leaf page key size" : 3276,
					"maximum leaf page size" : 32768,
					"maximum leaf page value size" : 1048576,
					"overflow pages" : 0,
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				},
				"cache" : {
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					"bytes written from cache" : 220177857469,
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					"unmodified pages evicted" : 18673872,
					"page split during eviction deepened the tree" : 0,
					"modified pages evicted" : 16975859,
					"data source pages selected for eviction unable to be evicted" : 265551,
					"hazard pointer blocked page eviction" : 29785,
					"internal pages evicted" : 1942243,
					"pages split during eviction" : 2553415,
					"in-memory page splits" : 13,
					"overflow values cached in memory" : 0,
					"pages read into cache" : 37187475,
					"overflow pages read into cache" : 0,
					"pages written from cache" : 22218833
				},
				"compression" : {
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					"raw compression call failed, additional data available" : 0,
					"raw compression call succeeded" : 0,
					"compressed pages read" : 9016031,
					"compressed pages written" : 6680487,
					"page written failed to compress" : 15,
					"page written was too small to compress" : 15517433
				},
				"cursor" : {
					"create calls" : 129,
					"insert calls" : 60227766,
					"bulk-loaded cursor-insert calls" : 0,
					"cursor-insert key and value bytes inserted" : 57222394251,
					"next calls" : 123498076,
					"prev calls" : 1,
					"remove calls" : 484963,
					"cursor-remove key bytes removed" : 2424815,
					"reset calls" : 519482966,
					"search calls" : 516615376,
					"search near calls" : 1234589,
					"update calls" : 0,
					"cursor-update value bytes updated" : 0
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					"internal page multi-block writes" : 120860,
					"leaf page multi-block writes" : 3237174,
					"maximum blocks required for a page" : 229,
					"internal-page overflow keys" : 0,
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					"overflow values written" : 0,
					"pages deleted" : 18189,
					"page checksum matches" : 327349,
					"page reconciliation calls" : 19144821,
					"page reconciliation calls for eviction" : 8629193,
					"leaf page key bytes discarded using prefix compression" : 0,
					"internal page key bytes discarded using suffix compression" : 3288866
				},
				"session" : {
					"object compaction" : 1,
					"open cursor count" : 129
				},
				"transaction" : {
					"update conflicts" : 150
				}
			},
			"nindexes" : 16,
			"totalIndexSize" : 4669931520,
			"indexSizes" : {
				"_id_" : 477245440,
				"timestamp_-1" : 457199616,
				"_id_hashed" : 1010360320,
				"session_id_1" : 292364288,
				"event_type_1" : 136859648,
				"geo:ip_1" : 132878336,
				"geo:tag_1" : 373174272,
				"lat_1" : 236621824,
				"geo:tag_1_lat_1" : 522412032,
				"geo:ip_1_ip_1" : 130265088,
				"session_id_-1" : 311750656,
				"event_day_1" : 125517824,
				"event_name_1" : 127680512,
				"rep_name_1" : 130445312,
				"app_slug_1" : 102637568,
				"app_name_1" : 102518784
			},
			"ok" : 1,
			"$gleStats" : {
				"lastOpTime" : Timestamp(0, 0),
				"electionId" : ObjectId("55701b9369ebc9d4c49ca64b")
			}
		},
		"eventsdata_1" : {
			"ns" : "events.all_events",
			"count" : 27227193,
			"size" : 26245228935,
			"avgObjSize" : 963,
			"storageSize" : 27254431744,
			"capped" : false,
			"wiredTiger" : {
				"metadata" : {
					"formatVersion" : 1
				},
				"creationString" : "allocation_size=4KB,app_metadata=(formatVersion=1),block_allocation=best,block_compressor=snappy,cache_resident=0,checkpoint=(WiredTigerCheckpoint.15552=(addr=\"01e365678881e4bc3ce7a0e365678989e4849c1fade365679287e4ac995290808080e506587d7fc0e5065a9b2fc0\",order=15552,time=1433843240,size=27289931776,write_gen=44251876)),checkpoint_lsn=(1644,12731648),checksum=on,collator=,columns=,dictionary=0,format=btree,huffman_key=,huffman_value=,id=61,internal_item_max=0,internal_key_max=0,internal_key_truncate=,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=1MB,memory_page_max=10m,os_cache_dirty_max=0,os_cache_max=0,prefix_compression=0,prefix_compression_min=4,split_deepen_min_child=0,split_deepen_per_child=0,split_pct=90,value_format=u,version=(major=1,minor=1)",
				"type" : "file",
				"uri" : "statistics:table:collection-58--4986008670220290220",
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					"bloom filter false positives" : 0,
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					"bloom filter misses" : 0,
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					"sleep for LSM checkpoint throttle" : 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 merge throttle" : 0
				},
				"block-manager" : {
					"file allocation unit size" : 4096,
					"blocks allocated" : 20108507,
					"checkpoint size" : 27289931776,
					"allocations requiring file extension" : 1930258,
					"blocks freed" : 17617959,
					"file magic number" : 120897,
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					"file bytes available for reuse" : 28123136,
					"file size in bytes" : 27254431744
				},
				"btree" : {
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					"pages rewritten by compaction" : 0,
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				"cache" : {
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					"bytes written from cache" : 207213945325,
					"checkpoint blocked page eviction" : 2405,
					"unmodified pages evicted" : 119030148,
					"page split during eviction deepened the tree" : 0,
					"modified pages evicted" : 14771534,
					"data source pages selected for eviction unable to be evicted" : 595764,
					"hazard pointer blocked page eviction" : 63559,
					"internal pages evicted" : 7003431,
					"pages split during eviction" : 2492884,
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					"pages read into cache" : 135693272,
					"overflow pages read into cache" : 0,
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				"compression" : {
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					"compressed pages read" : 47925700,
					"compressed pages written" : 6352132,
					"page written failed to compress" : 7,
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					"bulk-loaded cursor-insert calls" : 0,
					"cursor-insert key and value bytes inserted" : 61026252965,
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					"cursor-remove key bytes removed" : 2413220,
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					"open cursor count" : 196
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			"nindexes" : 16,
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			"indexSizes" : {
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				"_id_hashed" : 988872704,
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				"geo:ip_1_ip_1" : 127283200,
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				"geo:tag_1" : 367271936,
				"lat_1" : 230047744,
				"session_id_-1" : 286044160,
				"event_day_1" : 85929984,
				"event_name_1" : 90054656,
				"rep_name_1" : 127033344,
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			"$gleStats" : {
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				"electionId" : ObjectId("5568836aa7bea53384d0fc1f")
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		"eventsdata_2" : {
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			"capped" : false,
			"wiredTiger" : {
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				"creationString" : "allocation_size=4KB,app_metadata=(formatVersion=1),block_allocation=best,block_compressor=snappy,cache_resident=0,checkpoint=(WiredTigerCheckpoint.15672=(addr=\"01e3610c5481e4cf1c0d37e3610c5589e4ac8099f5e3610c5e88e4290d64fa808080e50612ca4fc0e50614e1efc0\",order=15672,time=1433843204,size=26120163328,write_gen=43301047)),checkpoint_lsn=(1518,43264256),checksum=on,collator=,columns=,dictionary=0,format=btree,huffman_key=,huffman_value=,id=41,internal_item_max=0,internal_key_max=0,internal_key_truncate=,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=1MB,memory_page_max=10m,os_cache_dirty_max=0,os_cache_max=0,prefix_compression=0,prefix_compression_min=4,split_deepen_min_child=0,split_deepen_per_child=0,split_pct=90,value_format=u,version=(major=1,minor=1)",
				"type" : "file",
				"uri" : "statistics:table:collection-38--4758915455553837045",
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					"queries that could have benefited from a Bloom filter that did not exist" : 0,
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				"block-manager" : {
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					"blocks allocated" : 20007715,
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					"allocations requiring file extension" : 1840000,
					"blocks freed" : 17509748,
					"file magic number" : 120897,
					"file major version number" : 1,
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					"file bytes available for reuse" : 14958592,
					"file size in bytes" : 26085060608
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				"btree" : {
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					"column-store variable-size leaf pages" : 0,
					"pages rewritten by compaction" : 0,
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					"maximum internal page size" : 4096,
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					"maximum leaf page value size" : 1048576,
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				},
				"cache" : {
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					"bytes written from cache" : 214974364993,
					"checkpoint blocked page eviction" : 1830,
					"unmodified pages evicted" : 520408127,
					"page split during eviction deepened the tree" : 0,
					"modified pages evicted" : 15758351,
					"data source pages selected for eviction unable to be evicted" : 1261235,
					"hazard pointer blocked page eviction" : 115697,
					"internal pages evicted" : 41888306,
					"pages split during eviction" : 2485582,
					"in-memory page splits" : 9,
					"overflow values cached in memory" : 0,
					"pages read into cache" : 538619641,
					"overflow pages read into cache" : 0,
					"pages written from cache" : 19993127
				},
				"compression" : {
					"raw compression call failed, no additional data available" : 0,
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					"raw compression call succeeded" : 0,
					"compressed pages read" : 349796855,
					"compressed pages written" : 6559455,
					"page written failed to compress" : 7,
					"page written was too small to compress" : 13413462
				},
				"cursor" : {
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					"insert calls" : 59528280,
					"bulk-loaded cursor-insert calls" : 0,
					"cursor-insert key and value bytes inserted" : 55101367028,
					"next calls" : 1078490462,
					"prev calls" : 1,
					"remove calls" : 794216,
					"cursor-remove key bytes removed" : 3971080,
					"reset calls" : 17624036869,
					"search calls" : 17518195588,
					"search near calls" : 8563891,
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					"cursor-update value bytes updated" : 0
				},
				"reconciliation" : {
					"dictionary matches" : 0,
					"internal page multi-block writes" : 100200,
					"leaf page multi-block writes" : 2826868,
					"maximum blocks required for a page" : 305,
					"internal-page overflow keys" : 0,
					"leaf-page overflow keys" : 0,
					"overflow values written" : 0,
					"pages deleted" : 37909,
					"page checksum matches" : 127368,
					"page reconciliation calls" : 17182624,
					"page reconciliation calls for eviction" : 7516665,
					"leaf page key bytes discarded using prefix compression" : 0,
					"internal page key bytes discarded using suffix compression" : 2875738
				},
				"session" : {
					"object compaction" : 0,
					"open cursor count" : 383
				},
				"transaction" : {
					"update conflicts" : 2776993
				}
			},
			"nindexes" : 16,
			"totalIndexSize" : 4369416192,
			"indexSizes" : {
				"_id_" : 420839424,
				"timestamp_-1" : 392732672,
				"_id_hashed" : 884072448,
				"session_id_1" : 273289216,
				"event_type_1" : 159678464,
				"geo:ip_1" : 152477696,
				"geo:tag_1" : 362020864,
				"lat_1" : 218329088,
				"geo:tag_1_lat_1" : 507912192,
				"geo:ip_1_ip_1" : 151433216,
				"session_id_-1" : 274432000,
				"event_day_1" : 83247104,
				"event_name_1" : 96964608,
				"rep_name_1" : 128393216,
				"app_slug_1" : 98181120,
				"app_name_1" : 165412864
			},
			"ok" : 1,
			"$gleStats" : {
				"lastOpTime" : Timestamp(0, 0),
				"electionId" : ObjectId("55688369b122e7008bcbb4f2")
			}
		}
	},
	"ok" : 1
}

5. they start with something like this:

{ "_id" : ObjectId("5576b735bbf9075bdf5b061a"), "week_of_year" : "CW23", "event_type" : "scroll", "timestamp" : ISODate("2015-06-09T09:51:44.956Z"), "event_year" : 2015, "lat" : "40.180447", "session_id" : "1433843156267", "device" : "000-ffffffff-ae44-0572-0000-0000136f1cc8", "_lock_expire" : ISODate("2015-06-09T09:51:49.034Z"), "quarter" : "Q2", "app_type" : "android", "_last_modified" : ISODate("2015-06-09T09:51:49.034Z"), "lon" : "29.1215119", "day_of_month" : 9, "_lock_id" : 0, "params" : "{\"realPage\":\"1\",\"chapterName\":\"null\",\"page\":\"61\",\"presentation\":\"88662_1432812946\",\"presentationName\"}", "event_day" : "Tuesday", "month_of_year" : 6, "event_extra" : "", "_created" : ISODate("2015-06-09T09:51:48Z"), "_status" : "new", "app_version" : 22, "event_month" : "June", "app_slug" : "antares_ipek" }

and get enriched to something like this:

{ "_id" : ObjectId("555b41b841480f5fb09ec98a"), "week_of_year" : "CW50", "event_type" : "activate", "timestamp" : ISODate("2013-12-20T12:09:14.649Z"), "event_year" : 2013, "lat" : "36.8577934", "session_id" : "1387540459306", "device" : "000-ffffffff-e03b-15bd-0000-000013a7836a", "_lock_expire" : ISODate("2015-05-19T13:59:20.758Z"), "quarter" : "Q4", "app_type" : "android", "_last_modified" : ISODate("2015-05-19T13:59:20.758Z"), "lon" : "30.9127808", "day_of_month" : 20, "_lock_id" : 0, "params" : "", "event_day" : "Friday", "month_of_year" : 12, "event_extra" : "", "_created" : ISODate("2013-12-23T11:04:55Z"), "_status" : "new", "app_version" : 10, "event_month" : "December", "app_slug" : "asteria_melis", "geo:tag" : { "country_iso_code" : "TR", "area_name" : "Antalya", "full_address" : "Unnamed Road, 07110 Antalya, Turkey", "street" : "Unnamed Road", "postal_code" : "07110", "area_iso_code" : "Antalya", "country_name" : "Turkey" }, "rep_name" : "504627", "event_name" : "", "licence_id" : 240, "app_name" : "Aİ Asteria", "app_id" : null }

6. i don't have a dir listening before the diskspace

Comment by Ramon Fernandez Marina [ 05/Jun/15 ]

digi604, can you please provide additional details about your setup so we can reproduce this behavior on our end? In particular:

  1. Version of MongoDB you're using
  2. Deployment details (stand-alone, replica set, etc.)
  3. Full logs for the node where you see the large increase in disk space
  4. Some details about your documents; some sample documents and the output of db.collection.stats() would be ideal
  5. Some information about the updates that these documents go through
  6. A directory listing of your dbpath before and after the disk space

Thanks,
Ramón.

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