Short repro: $ ./mongod --replSet replSet --dbpath ~/Temp/Data/replSet/ --logpath ~/Temp/Data/replSet/mongod.log --setParameter logicalSessionRefreshMillis=10 --setParameter localLogicalSessionTimeoutMinutes=0 --fork $ ./mongo replSet:SECONDARY> rs.initiate(); ... replSet:PRIMARY> db.shutdownServer({force:true}); ... $ ./mongod --replSet replSet --dbpath ~/Temp/Data/replSet/ --logpath ~/Temp/Data/replSet/mongod.log --setParameter logicalSessionRefreshMillis=10 --setParameter localLogicalSessionTimeoutMinutes=3 --fork This produces the said message in the log: 2018-10-11T15:53:35.906+0000 I COMMAND [LogicalSessionCacheRefresh] command config.$cmd command: createIndexes { createIndexes: "system.sessions", indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex", expireAfterSeconds: 7800 } ], $db: "config" } numYields:0 ok:0 errMsg:"Index with name: lsidTTLIndex already exists with different options" errName:IndexOptionsConflict errCode:85 reslen:163 locks:{ Global: { acquireCount: { r: 2, w: 2 } }, Database: { acquireCount: { w: 2 } }, Collection: { acquireCount: { w: 1 } } } protocol:op_msg 0ms 2018-10-11T15:53:35.906+0000 I CONTROL [LogicalSessionCacheRefresh] Sessions collection is not set up; waiting until next sessions refresh interval: Index with name: lsidTTLIndex already exists with different options From reporter: 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] MongoDB starting : pid=15496 port=27017 dbpath=/data/test-standalone 64-bit host=mmovh6.milanamos.net 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] db version v4.0.3 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] git version: 7ea530946fa7880364d88c8d8b6026bbc9ffa48c 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.0g 2 Nov 2017 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] allocator: tcmalloc 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] modules: none 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] build environment: 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] distmod: ubuntu1804 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] distarch: x86_64 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] target_arch: x86_64 2018-10-11T13:33:34.566+0000 I CONTROL [initandlisten] options: { config: "/data/test-standalone/automation-mongod.conf" , net: { bindIp: "0.0.0.0" , bindIpAll: true , port: 27017 }, op erationProfiling: { mode: "slowOp" , slowOpThresholdMs: 100 }, processManagement: { fork: true }, security: { authorization: "enabled" , keyFile: "/ var /lib/mongodb-mms-automation/keyfil e " }, setParameter: { authenticationMechanisms: " SCRAM-SHA-1,SCRAM-SHA-256 ", cursorTimeoutMillis: " 7200000 ", localLogicalSessionTimeoutMinutes: " 130 " }, storage: { dbPath: " /data/test -standalone ", engine: " wiredTiger " }, systemLog: { destination: " file ", path: " /data/test-standalone/mongodb.log" } } [...] 2018-10-11T15:53:35.906+0000 D COMMAND [LogicalSessionCacheRefresh] run command config.$cmd { createIndexes: "system.sessions" , indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex" , expireAfterSeconds: 7800 } ], $db: "config" } 2018-10-11T15:53:35.906+0000 D STORAGE [LogicalSessionCacheRefresh] NamespaceUUIDCache: registered namespace config.system.sessions with UUID 8536711e-8cae-4309-9de1-e73aa77c7ae0 2018-10-11T15:53:35.906+0000 D - [LogicalSessionCacheRefresh] User Assertion: IndexOptionsConflict: Index with name: lsidTTLIndex already exists with different options src/mongo/db/commands/create_indexes.cpp 230 2018-10-11T15:53:35.906+0000 D REPL [LogicalSessionCacheRefresh] Waiting for write concern. OpTime: { ts: Timestamp(0, 0), t: -1 }, write concern: { w: 1, wtimeout: 0 } 2018-10-11T15:53:35.906+0000 D COMMAND [LogicalSessionCacheRefresh] assertion while executing command 'createIndexes' on database 'config' with arguments '{ createIndexes: "system.sessions" , indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex" , expireAfterSeconds: 7800 } ], $db: "config" }' : IndexOptionsConflict: Index with name: lsidTTLIndex already exists with different options 2018-10-11T15:53:35.906+0000 I COMMAND [LogicalSessionCacheRefresh] command config.$cmd command: createIndexes { createIndexes: "system.sessions" , indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex" , expireAfterSeconds: 7800 } ], $db: "config" } numYields:0 ok:0 errMsg: "Index with name: lsidTTLIndex already exists with different options" errName:IndexOptionsConflict errCode:85 reslen:163 locks:{ Global: { acquireCount: { r: 2, w: 2 } }, Database: { acquireCount: { w: 2 } }, Collection: { acquireCount: { w: 1 } } } protocol:op_msg 0ms 2018-10-11T15:53:35.906+0000 I CONTROL [LogicalSessionCacheRefresh] Sessions collection is not set up; waiting until next sessions refresh interval: Index with name: lsidTTLIndex already exists with different options and in mongo today: > new Date() ISODate( "2018-10-15T08:21:27.022Z" ) > db.aggregate([{$listLocalSessions: {allUsers: true }}]) { "_id" : { "id" : UUID( "3a86b514-a453-478f-810d-8f2dd4c057ca" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-12T13:17:38.818Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "489ea100-fb41-4e4e-bd0b-623c86c46102" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:22:49.169Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "ede7ecab-9ea2-4106-ba8f-27de7add92e6" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:34:44.824Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "0de2fde6-253c-4ccc-b6c9-b5ca65ec494e" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:23:50.855Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "dd73b620-2b82-4d64-b296-4c2fbe8b2495" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-12T13:17:16.084Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "f680077a-824a-4cf3-b970-e05f6aa5b2f6" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:10:38.579Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "35cbc73b-5796-491f-8d80-415e25a2d552" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-12T13:17:40.570Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "ed918f82-383c-4162-97f2-a90bde93374c" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-12T13:17:14.419Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "cb3b4bff-3462-4d8a-a228-bd8de31d4503" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:36:39.143Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "8a3f879a-22b7-4c4e-96dc-c4a630b50ac0" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:35:50.095Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "c39c5f57-ad0d-480b-bac4-540d9ae75fd2" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:34:43.173Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "592f7a6a-c643-4781-a657-8e597a02ee95" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:33:50.600Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "b375b3a8-8fd3-48b0-b43c-c61341759c03" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:32:03.184Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "0192ff36-9430-4262-ad7e-62fe0bd35d69" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:33:48.904Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "89625c86-64e0-4409-a6e6-c82136aed279" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:26:09.546Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "a7c81832-940f-4c8d-ac47-8b66a66b043f" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:16:37.304Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "78c2256b-7e1d-4a3a-97bf-5b87dfd472e5" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:15:35.193Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "4d7ad3f5-e8c8-4631-bca7-9180fc1eb5ec" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-12T14:00:32.620Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "bdb7f93d-7966-4ba9-8223-f85592e89e34" ), "uid" : BinData(0, "gvI6E3rwpLEMfFQo/pac02FLjxJ9+Zfrt+aIKnzCZeE=" ) }, "lastUse" : ISODate( "2018-10-11T15:25:07.802Z" ), "user" : "adminMongo@admin" } { "_id" : { "id" : UUID( "0361c9da-f881-4eaa-be95-4015178cfba2" ), "uid" : BinData(0, "7D7UuwqwK21uSTtaadvqpdytlQ+wwVZnZdE3WGwp8Uk=" ) }, "lastUse" : ISODate( "2018-10-11T15:04:00.289Z" ), "user" : "optimodeWrite@optimode" } Type "it" for more >