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    Type:
Bug
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    Resolution: Done
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    Priority:
Critical - P2
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    Affects Version/s: 3.0.0
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    Component/s: Replication, WiredTiger
 
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        Fully Compatible
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        ALL
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        None
 
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        None
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        None
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        None
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        None
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        None
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        None
 
after re-sync is done, the _id index count, secondary index count and data table count could be different.
"index" : 2000000, "secondary_index" : 2047102, "table" : 2047102
and log file show (with Dan's patch for more printout)
2015-03-06T01:05:28.851+0000 I REPL     [rsSync] ******
2015-03-06T01:05:28.851+0000 I REPL     [rsSync] creating replication oplog of size: 4094MB...
2015-03-06T01:05:28.853+0000 I STORAGE  [rsSync] Starting WiredTigerRecordStoreThread local.oplog.rs
2015-03-06T01:05:28.870+0000 I REPL     [rsSync] ******
2015-03-06T01:05:28.870+0000 I REPL     [rsSync] initial sync pending
2015-03-06T01:05:28.870+0000 I REPL     [ReplicationExecutor] syncing from: 10.1.1.107:27017
2015-03-06T01:05:28.874+0000 I REPL     [rsSync] initial sync drop all databases
2015-03-06T01:05:28.874+0000 I STORAGE  [rsSync] dropAllDatabasesExceptLocal 1
2015-03-06T01:05:28.874+0000 I REPL     [rsSync] initial sync clone all databases
2015-03-06T01:05:28.875+0000 I REPL     [rsSync] initial sync cloning db: sbtest
2015-03-06T01:05:42.605+0000 I INDEX    [rsSync] build index on: sbtest.sbtest1 properties: { v: 1, key: { _id: 1 }, name: "_id_", ns: "sbtest.sbtest1" }
2015-03-06T01:05:42.605+0000 I INDEX    [rsSync]         building index using bulk method
2015-03-06T01:05:47.969+0000 I INDEX    [rsSync] build index done.  scanned 2047128 total records. 5 secs
2015-03-06T01:05:47.969+0000 I STORAGE  [rsSync] Deleting: RecordId(1955618)
2015-03-06T01:05:47.969+0000 I STORAGE  [rsSync] Deleting: RecordId(1955661)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1955710)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1955778)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1955802)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1955996)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1956089)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1956102)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1956127)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1956187)
2015-03-06T01:05:47.970+0000 I STORAGE  [rsSync] Deleting: RecordId(1956305)
....
2015-03-06T01:05:49.275+0000 I STORAGE  [rsSync] Deleting: RecordId(2047128)
2015-03-06T01:05:49.275+0000 I STORAGE  [rsSync] index build dropped: 47128 dups
2015-03-06T01:05:49.449+0000 I REPL     [rsSync] initial sync data copy, starting syncup
2015-03-06T01:05:49.449+0000 I REPL     [rsSync] oplog sync 1 of 3
- not sure why there is dup for _id
 - dropped dups are not removed from data table and secondary index tree
 - saw one case when mixed traffic stopped, re-sync still have issue with dups and out of sync, but cannot reproduce it now.