Fatal Assertion 40292 while configuring replica set (v4.2.10)

Facing following error while configuring the replica set.

2021-01-06T10:09:12.674+0000 I  CONTROL  [main] ***** SERVER RESTARTED *****
2021-01-06T10:09:12.679+0000 I  CONTROL  [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
2021-01-06T10:09:12.681+0000 W  ASIO     [main] No TransportLayer configured during NetworkInterface startup
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] MongoDB starting : pid=14056 port=37017 dbpath=/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/data 64-bit host=ip-10-122-8-237.us-west-2.compute.internal
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] db version v4.2.10
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] git version: 88276238fa97b47c0ef14362b343c5317ecbd739
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2k-fips  26 Jan 2017
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] allocator: tcmalloc
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] modules: none
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] build environment:
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten]     distmod: amazon
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten]     distarch: x86_64
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten]     target_arch: x86_64
2021-01-06T10:09:12.750+0000 I  CONTROL  [initandlisten] options: { config: "/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/mongod.conf", net: { bindIp: "localhost,10.122.8.237", port: 37017 }, processManagement: { fork: true }, replication: { enableMajorityReadConcern: false, oplogSizeMB: 100000, replSetName: "avfmrs" }, security: { authorization: "enabled", keyFile: "/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/key/mongoKey" }, storage: { dbPath: "/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/data", engine: "wiredTiger", journal: { enabled: true } }, systemLog: { destination: "file", logAppend: true, logRotate: "reopen", path: "/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/logs/mongo.log" } }
2021-01-06T10:09:12.753+0000 I  STORAGE  [initandlisten] wiredtiger_open config: create,cache_size=3292M,cache_overflow=(file_max=0M),session_max=33000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000,close_scan_interval=10,close_handle_minimum=250),statistics_log=(wait=0),verbose=[recovery_progress,checkpoint_progress],
2021-01-06T10:09:13.318+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:318114][14056:0x7fd076be1c40], txn-recover: Recovering log 8909 through 8910
2021-01-06T10:09:13.377+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:377076][14056:0x7fd076be1c40], txn-recover: Recovering log 8910 through 8910
2021-01-06T10:09:13.513+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:513533][14056:0x7fd076be1c40], txn-recover: Main recovery loop: starting at 8909/39040 to 8910/256
2021-01-06T10:09:13.514+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:514945][14056:0x7fd076be1c40], txn-recover: Recovering log 8909 through 8910
2021-01-06T10:09:13.605+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:605598][14056:0x7fd076be1c40], txn-recover: Recovering log 8910 through 8910
2021-01-06T10:09:13.662+0000 I  STORAGE  [initandlisten] WiredTiger message [1609927753:662821][14056:0x7fd076be1c40], txn-recover: Set global recovery timestamp: (1609910372, 1)
2021-01-06T10:09:13.676+0000 I  RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(1609910372, 1)
2021-01-06T10:09:17.294+0000 I  STORAGE  [initandlisten] Starting OplogTruncaterThread local.oplog.rs
2021-01-06T10:09:17.294+0000 I  STORAGE  [initandlisten] The size storer reports that the oplog contains 56 records totaling to 7124 bytes
2021-01-06T10:09:17.294+0000 I  STORAGE  [initandlisten] Scanning the oplog to determine where to place markers for truncation
2021-01-06T10:09:17.295+0000 I  STORAGE  [initandlisten] WiredTiger record store oplog processing took 0ms
2021-01-06T10:09:17.305+0000 I  STORAGE  [initandlisten] Timestamp monitor starting
2021-01-06T10:09:41.883+0000 I  SHARDING [initandlisten] Marking collection local.system.replset as collection version: <unsharded>
2021-01-06T10:09:41.886+0000 I  STORAGE  [initandlisten] Flow Control is enabled on this deployment.
2021-01-06T10:09:41.886+0000 I  SHARDING [initandlisten] Marking collection admin.system.roles as collection version: <unsharded>
2021-01-06T10:09:41.887+0000 I  SHARDING [initandlisten] Marking collection admin.system.version as collection version: <unsharded>
2021-01-06T10:09:41.888+0000 I  SHARDING [initandlisten] Marking collection local.startup_log as collection version: <unsharded>
2021-01-06T10:09:41.889+0000 I  FTDC     [initandlisten] Initializing full-time diagnostic data capture with directory '/avfm-fo/mongodb-linux-x86_64-amazon-4.2.10/data/diagnostic.data'
2021-01-06T10:09:41.890+0000 I  SHARDING [initandlisten] Marking collection local.replset.minvalid as collection version: <unsharded>
2021-01-06T10:09:41.890+0000 I  SHARDING [initandlisten] Marking collection local.replset.election as collection version: <unsharded>
2021-01-06T10:09:41.891+0000 I  REPL     [initandlisten] Did not find local Rollback ID document at startup. Creating one.
2021-01-06T10:09:41.891+0000 I  STORAGE  [initandlisten] createCollection: local.system.rollback.id with generated UUID: fb814c0d-2acc-4b7f-b6c2-009b466da3f9 and options: {}
2021-01-06T10:09:41.891+0000 I  SHARDING [monitoring-keys-for-HMAC] Marking collection admin.system.keys as collection version: <unsharded>
2021-01-06T10:09:42.033+0000 I  INDEX    [initandlisten] index build: done building index _id_ on ns local.system.rollback.id
2021-01-06T10:09:42.033+0000 I  SHARDING [ftdc] Marking collection local.oplog.rs as collection version: <unsharded>
2021-01-06T10:09:42.033+0000 I  SHARDING [initandlisten] Marking collection local.system.rollback.id as collection version: <unsharded>
2021-01-06T10:09:42.033+0000 I  REPL     [initandlisten] Initialized the rollback ID to 1
2021-01-06T10:09:42.034+0000 I  REPL     [initandlisten] Recovering from stable timestamp: Timestamp(1609910372, 1) (top of oplog: { ts: Timestamp(1609927746, 1), t: 1 }, appliedThrough: { ts: Timestamp(0, 0), t: -1 }, TruncateAfter: Timestamp(0, 0))
2021-01-06T10:09:42.034+0000 I  REPL     [initandlisten] Starting recovery oplog application at the stable timestamp: Timestamp(1609910372, 1)
2021-01-06T10:09:42.034+0000 I  REPL     [initandlisten] Replaying stored operations from Timestamp(1609910372, 1) (inclusive) to Timestamp(1609927746, 1) (inclusive).
2021-01-06T10:09:42.034+0000 F  REPL     [initandlisten] Oplog entry at { : Timestamp(1609910372, 1) } is missing; actual entry found is { : Timestamp(1609927216, 1) }
2021-01-06T10:09:42.034+0000 F  -        [initandlisten] Fatal Assertion 40292 at src/mongo/db/repl/replication_recovery.cpp 149
2021-01-06T10:09:42.034+0000 F  -        [initandlisten]

***aborting after fassert() failure

Welcome to the MongoDB community @Amit_G!

Can you provide some more information on the steps you have taken leading up to this error? For example, are you adding this replica set member using a backup of files from another member?

The startup log messages indicate recovery from existing data files, so I would suspect an inconsistent file copy backup (perhaps from a running mongod?) or an unexpected shutdown.

The most straightforward approach to resolve this would be to remove the contents of the dbPath from this member to automatically sync using the initial sync process.

Regards,
Stennie

Hello @Stennie,

Thanks for looking into it.

Issue/Scenario:
I am using the filesystem backup/snapshot and configuring the mongodb relica set (PSA).

steps:
0. drop the local database from all three nodes (PSA)

  1. configure arbiter instance.
  2. configure Primary instance.
  3. configure replica set with arbiter instance and Secondary instance.
  4. take the dump of local db from Primary.
  5. restore the local dump on secondary.
  6. re-start the mongo service on Secondary → this is where I get the issue.

are you adding this replica set member using a backup of files from another member?
Yes,

automatically sync process is too slow and takes longer time. Hence that is not the viable option for us.
I use the same steps with 3.6.8 and it is all working fine since more than a year now.
Now I am using the same steps for 4.2.10 and it is failing.

Screenshot of the error:

Kindly advise.

Thanks in advance

Hi @Amit_G,

This is likely where things are going astray: if you take a backup of files that are actively being written to, you may get an inconsistent copy of the dbPath which is not usable.

Can you provide more detail on the exact actions you are taking between step 3 & 4, and in step 4?

You mentioned using filesystem backup/snapshot, so I’m interpreting your description as taking a filesystem snapshot rather than a mongodump.

If you are backing up with cp or rsync (i.e. a file copy rather than a filesystem snapshot), you need to stop any writes using db.syncLock() or by shutting mongod before copying the data files:

If your storage system does not support snapshots, you can copy the files directly using cp, rsync, or a similar tool. Since copying multiple files is not an atomic operation, you must stop all writes to the mongod before copying the files. Otherwise, you will copy the files in an invalid state.

Regards,
Stennie