I've a big collection, about 1.2bi documents, and I tried to create an index on this collection. I reproduced this bug with several fields.

• I'm using 4.1.6 version on docker, running in a Linux 4.9.0-8 server.
• This error happens even if starting the database in repair mode
• I didn't test inserting documents with the index already on the collection. I will need about 80 hours to reproduce if you need me to test this behavior.
• Marked the bug as blocking because other people with the same kind of bug won't be able to use their data, in a collection of this size, is not feasible to be used without an index.

Bellow the logs of the crash:

 

2018-12-22T21:25:04.993+0000 I INDEX [conn8] build index on: dashboard.delivery properties: { v: 2, unique: true, key:

{ address: 1.0 }

, name: "address_1", ns: "dashboard.delivery" }
2018-12-22T21:25:05.003+0000 I INDEX [conn8] building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2018-12-22T21:25:08.003+0000 I - [conn8] Index Build: 3735700/1271300000 0%
2018-12-22T21:25:11.003+0000 I - [conn8] Index Build: 7304300/1271300000 0%
...................
2018-12-22T22:01:05.006+0000 I - [conn8] Index Build: 1263292400/1271300000 99%
2018-12-22T22:01:08.003+0000 I - [conn8] Index Build: 1266345200/1271300000 99%
2018-12-22T22:01:17.474+0000 I - [conn8] Index Build: 1268605900/1271300000 99%
2018-12-22T22:01:20.003+0000 I - [conn8] Index Build: 1270923800/1271300000 99%
2018-12-22T22:01:32.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 17998500/1271300000 1%
2018-12-22T22:01:42.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 40824000/1271300000 3%
2018-12-22T22:01:52.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 63361700/1271300000 4%
2018-12-22T22:02:02.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 84591300/1271300000 6%
2018-12-22T22:02:12.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 108159600/1271300000 8%
2018-12-22T22:02:22.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 129773100/1271300000 10%
2018-12-22T22:02:32.018+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 152750600/1271300000 12%
2018-12-22T22:02:42.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 174621400/1271300000 13%
2018-12-22T22:02:52.007+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 197153900/1271300000 15%
2018-12-22T22:03:02.008+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 219340800/1271300000 17%
2018-12-22T22:03:12.007+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 241072500/1271300000 18%
2018-12-22T22:03:22.007+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 262647400/1271300000 20%
2018-12-22T22:03:32.019+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 284618500/1271300000 22%
2018-12-22T22:03:42.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 306719600/1271300000 24%
2018-12-22T22:03:52.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 329286200/1271300000 25%
2018-12-22T22:04:02.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 351621900/1271300000 27%
2018-12-22T22:04:12.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 374338500/1271300000 29%
2018-12-22T22:04:22.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 396971400/1271300000 31%
2018-12-22T22:04:32.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 419309500/1271300000 32%
2018-12-22T22:04:42.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 439332200/1271300000 34%
2018-12-22T22:04:52.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 461051300/1271300000 36%
2018-12-22T22:05:02.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 483465300/1271300000 38%
2018-12-22T22:05:12.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 505852400/1271300000 39%
2018-12-22T22:05:22.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 528176400/1271300000 41%
2018-12-22T22:05:32.003+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 550842500/1271300000 43%
2018-12-22T22:05:42.007+0000 I - [conn8] Index: (2/3) BTree Bottom Up Progress: 562153500/1271300000 44%
2018-12-22T22:05:49.186+0000 F - [conn8] Invariant failure static_cast<unsigned int>(_file.tellg()) == _fileEndOffset src/mongo/db/sorter/sorter.cpp 293
2018-12-22T22:05:49.218+0000 F - [conn8]

***aborting after invariant() failure

2018-12-22T22:05:49.597+0000 F - [conn8] Got signal: 6 (Aborted).
0x56187d1b1ef1 0x56187d1b1109 0x56187d1b15ed 0x7f3aa87e5390 0x7f3aa843f428 0x7f3aa844102a 0x56187b7843a3 0x56187c7fea78 0x56187c7feae1 0x56187c7ff0cb 0x56187c7fc91f 0x56187c7fa718 0x56187c002128 0x56187c002424 0x56187c001308 0x56187becc034 0x56187cb38356 0x56187cb3b534 0x56187bbf8e34 0x56187bbfb1ae 0x56187bbfc94c 0x56187bbfd926 0x56187bbe9b6a 0x56187bbf5f73 0x56187bbf1767 0x56187bbf5151 0x56187c95c0f2 0x56187bbef840 0x56187bbf2b85 0x56187bbf0d9f 0x56187bbf17ed 0x56187bbf5151 0x56187c95c665 0x56187d1077d4 0x7f3aa87db6ba 0x7f3aa851141d
----- BEGIN BACKTRACE -----

{"backtrace":[

{"b":"56187AD3F000","o":"2472EF1","s":"_ZN5mongo15printStackTraceERSo"}

,{"b":"56187AD3F000","o":"2472109"},{"b":"56187AD3F000","o":"24725ED"},{"b":"7F3AA87D4000","o":"11390"},{"b":"7F3AA840A000","o":"35428","s":"gsignal"},{"b":"7F3AA840A000","o":"3702A","s":"abort"},

{"b":"56187AD3F000","o":"A453A3","s":"_ZN5mongo22invariantFailedWithMsgEPKcRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES1_j"}

,{"b":"56187AD3F000","o":"1ABFA78","s":"_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE4readEPvm"},{"b":"56187AD3F000","o":"1ABFAE1","s":"_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE18fillBufferFromDiskEv"},{"b":"56187AD3F000","o":"1AC00CB","s":"_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE4moreEv"},{"b":"56187AD3F000","o":"1ABD91F","s":"_ZN5mongo6sorter13MergeIteratorINS_7BSONObjENS_8RecordIdENS_27BtreeExternalSortComparisonEE4moreEv"},{"b":"56187AD3F000","o":"1ABB718","s":"_ZN5mongo25AbstractIndexAccessMethod10commitBulkEPNS_16OperationContextEPNS_17IndexAccessMethod11BulkBuilderEbbPSt3setINS_8RecordIdESt4lessIS7_ESaIS7_EEPSt6vectorINS_7BSONObjESaISE_EE"},{"b":"56187AD3F000","o":"12C3128","s":"_ZN5mongo19MultiIndexBlockImpl20_dumpInsertsFromBulkEPSt3setINS_8RecordIdESt4lessIS2_ESaIS2_EEPSt6vectorINS_7BSONObjESaIS9_EE"},{"b":"56187AD3F000","o":"12C3424","s":"_ZN5mongo19MultiIndexBlockImpl19dumpInsertsFromBulkEv"},{"b":"56187AD3F000","o":"12C2308","s":"_ZN5mongo19MultiIndexBlockImpl30insertAllDocumentsInCollectionEv"},{"b":"56187AD3F000","o":"118D034"},

{"b":"56187AD3F000","o":"1DF9356","s":"_ZN5mongo23ErrmsgCommandDeprecated3runEPNS_16OperationContextERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7BSONObjERNS_14BSONObjBuilderE"}

,{"b":"56187AD3F000","o":"1DFC534","s":"_ZN5mongo12BasicCommand10Invocation3runEPNS_16OperationContextEPNS_3rpc21ReplyBuilderInterfaceE"},{"b":"56187AD3F000","o":"EB9E34"},{"b":"56187AD3F000","o":"EBC1AE"},{"b":"56187AD3F000","o":"EBD94C"},{"b":"56187AD3F000","o":"EBE926","s":"_ZN5mongo23ServiceEntryPointCommon13handleRequestEPNS_16OperationContextERKNS_7MessageERKNS0_5HooksE"},{"b":"56187AD3F000","o":"EAAB6A","s":"_ZN5mongo23ServiceEntryPointMongod13handleRequestEPNS_16OperationContextERKNS_7MessageE"},{"b":"56187AD3F000","o":"EB6F73","s":"_ZN5mongo19ServiceStateMachine15_processMessageENS0_11ThreadGuardE"},{"b":"56187AD3F000","o":"EB2767","s":"_ZN5mongo19ServiceStateMachine15_runNextInGuardENS0_11ThreadGuardE"},{"b":"56187AD3F000","o":"EB6151"},{"b":"56187AD3F000","o":"1C1D0F2","s":"_ZN5mongo9transport26ServiceExecutorSynchronous8scheduleESt8functionIFvvEENS0_15ServiceExecutor13ScheduleFlagsENS0_23ServiceExecutorTaskNameE"},{"b":"56187AD3F000","o":"EB0840","s":"_ZN5mongo19ServiceStateMachine22_scheduleNextWithGuardENS0_11ThreadGuardENS_9transport15ServiceExecutor13ScheduleFlagsENS2_23ServiceExecutorTaskNameENS0_9OwnershipE"},{"b":"56187AD3F000","o":"EB3B85","s":"_ZN5mongo19ServiceStateMachine15_sourceCallbackENS_6StatusE"},{"b":"56187AD3F000","o":"EB1D9F","s":"_ZN5mongo19ServiceStateMachine14_sourceMessageENS0_11ThreadGuardE"},{"b":"56187AD3F000","o":"EB27ED","s":"_ZN5mongo19ServiceStateMachine15_runNextInGuardENS0_11ThreadGuardE"},{"b":"56187AD3F000","o":"EB6151"},{"b":"56187AD3F000","o":"1C1D665"},{"b":"56187AD3F000","o":"23C87D4"},{"b":"7F3AA87D4000","o":"76BA"},{"b":"7F3AA840A000","o":"10741D","s":"clone"}],"processInfo":{ "mongodbVersion" : "4.1.6", "gitVersion" : "55e72b015e2aa7297c00db29e4d93451ea61a7ca", "compiledModules" : [], "uname" :

{ "sysname" : "Linux", "release" : "4.9.0-8-amd64", "version" : "#1 SMP Debian 4.9.130-2 (2018-10-27)", "machine" : "x86_64" }

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mongod(_ZN5mongo15printStackTraceERSo+0x41) [0x56187d1b1ef1]
mongod(+0x2472109) [0x56187d1b1109]
mongod(+0x24725ED) [0x56187d1b15ed]
libpthread.so.0(+0x11390) [0x7f3aa87e5390]
libc.so.6(gsignal+0x38) [0x7f3aa843f428]
libc.so.6(abort+0x16A) [0x7f3aa844102a]
mongod(ZN5mongo22invariantFailedWithMsgEPKcRKNSt7_cxx1112basic_stringIcSt11char_traitsIcESaIcEEES1_j+0x0) [0x56187b7843a3]
mongod(_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE4readEPvm+0xD8) [0x56187c7fea78]
mongod(_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE18fillBufferFromDiskEv+0x31) [0x56187c7feae1]
mongod(_ZN5mongo6sorter12FileIteratorINS_7BSONObjENS_8RecordIdEE4moreEv+0x3B) [0x56187c7ff0cb]
mongod(_ZN5mongo6sorter13MergeIteratorINS_7BSONObjENS_8RecordIdENS_27BtreeExternalSortComparisonEE4moreEv+0x3F) [0x56187c7fc91f]
mongod(_ZN5mongo25AbstractIndexAccessMethod10commitBulkEPNS_16OperationContextEPNS_17IndexAccessMethod11BulkBuilderEbbPSt3setINS_8RecordIdESt4lessIS7_ESaIS7_EEPSt6vectorINS_7BSONObjESaISE_EE+0x1E8) [0x56187c7fa718]
mongod(_ZN5mongo19MultiIndexBlockImpl20_dumpInsertsFromBulkEPSt3setINS_8RecordIdESt4lessIS2_ESaIS2_EEPSt6vectorINS_7BSONObjESaIS9_EE+0x1D8) [0x56187c002128]
mongod(_ZN5mongo19MultiIndexBlockImpl19dumpInsertsFromBulkEv+0x24) [0x56187c002424]
mongod(_ZN5mongo19MultiIndexBlockImpl30insertAllDocumentsInCollectionEv+0x8E8) [0x56187c001308]
mongod(+0x118D034) [0x56187becc034]
mongod(ZN5mongo23ErrmsgCommandDeprecated3runEPNS_16OperationContextERKNSt7_cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7BSONObjERNS_14BSONObjBuilderE+0x46) [0x56187cb38356]
mongod(_ZN5mongo12BasicCommand10Invocation3runEPNS_16OperationContextEPNS_3rpc21ReplyBuilderInterfaceE+0x74) [0x56187cb3b534]
mongod(+0xEB9E34) [0x56187bbf8e34]
mongod(+0xEBC1AE) [0x56187bbfb1ae]
mongod(+0xEBD94C) [0x56187bbfc94c]
mongod(_ZN5mongo23ServiceEntryPointCommon13handleRequestEPNS_16OperationContextERKNS_7MessageERKNS0_5HooksE+0x476) [0x56187bbfd926]
mongod(_ZN5mongo23ServiceEntryPointMongod13handleRequestEPNS_16OperationContextERKNS_7MessageE+0x3A) [0x56187bbe9b6a]
mongod(_ZN5mongo19ServiceStateMachine15_processMessageENS0_11ThreadGuardE+0xD3) [0x56187bbf5f73]
mongod(_ZN5mongo19ServiceStateMachine15_runNextInGuardENS0_11ThreadGuardE+0x97) [0x56187bbf1767]
mongod(+0xEB6151) [0x56187bbf5151]
mongod(_ZN5mongo9transport26ServiceExecutorSynchronous8scheduleESt8functionIFvvEENS0_15ServiceExecutor13ScheduleFlagsENS0_23ServiceExecutorTaskNameE+0x1A2) [0x56187c95c0f2]
mongod(_ZN5mongo19ServiceStateMachine22_scheduleNextWithGuardENS0_11ThreadGuardENS_9transport15ServiceExecutor13ScheduleFlagsENS2_23ServiceExecutorTaskNameENS0_9OwnershipE+0x150) [0x56187bbef840]
mongod(_ZN5mongo19ServiceStateMachine15_sourceCallbackENS_6StatusE+0xB55) [0x56187bbf2b85]
mongod(_ZN5mongo19ServiceStateMachine14_sourceMessageENS0_11ThreadGuardE+0x35F) [0x56187bbf0d9f]
mongod(_ZN5mongo19ServiceStateMachine15_runNextInGuardENS0_11ThreadGuardE+0x11D) [0x56187bbf17ed]
mongod(+0xEB6151) [0x56187bbf5151]
mongod(+0x1C1D665) [0x56187c95c665]
mongod(+0x23C87D4) [0x56187d1077d4]
libpthread.so.0(+0x76BA) [0x7f3aa87db6ba]
libc.so.6(clone+0x6D) [0x7f3aa851141d]
----- END BACKTRACE -----