We have a mongodb 3.4.0 pod running in a kubernetes cluster, we are trying to upgrade however this is blocking us. This pod runs for about 7 minutes before we see the following error:
2022-10-28T17:49:26.597+0000 E STORAGE [thread2] WiredTiger error (5) [1666979366:596967][1:0x7f187d54c700], log-server: /datastore/db/journal: directory-list: opendir: Input/output error
2022-10-28T17:49:26.597+0000 E STORAGE [thread2] WiredTiger error (5) [1666979366:597060][1:0x7f187d54c700], log-server: log pre-alloc server error: Input/output error
2022-10-28T17:49:26.597+0000 E STORAGE [thread2] WiredTiger error (5) [1666979366:597072][1:0x7f187d54c700], log-server: log server error: Input/output error
2022-10-28T17:49:31.001+0000 W FTDC [ftdc] Uncaught exception in 'FileNotOpen: Failed to open interim file /datastore/db/diagnostic.data/metrics.interim.temp' in full-time diagnostic data capture subsystem. Shutting down the full-time diagnostic data capture subsystem.
2022-10-28T17:51:53.882+0000 E STORAGE [WTJournalFlusher] WiredTiger error (5) [1666979513:882390][1:0x7f187ad48700], WT_SESSION.log_flush: /datastore/db/journal/WiredTigerLog.0000000671: handle-write: pwrite: failed to write 768 bytes at offset 11904: Input/output error
2022-10-28T17:51:53.882+0000 I - [WTJournalFlusher] Invariant failure: s->log_flush(s, "sync=on") resulted in status UnknownError: 5: Input/output error at src/mongo/db/storage/wiredtiger/wiredtiger_session_cache.cpp 229
2022-10-28T17:51:53.882+0000 I - [WTJournalFlusher]
***aborting after invariant() failure
This is the file it is referencing: mongo/wiredtiger_session_cache.cpp at r3.4.0 · mongodb/mongo · GitHub
We have ran a repair against MongoDB using the following command:
kubectl exec -it mongodb-0 – mongod --dbpath /data/db --port 27020 --bind_ip 0.0.0.0 --repair
Here is the output of that command:
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] MongoDB starting : pid=41 port=27020 dbpath=/data/db 64-bit host=mongodb-0
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] db version v3.4.0
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] git version: f4240c60f005be757399042dc12f6addbc3170c1
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.1t 3 May 2016
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] allocator: tcmalloc
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] modules: none
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] build environment:
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] distmod: debian81
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] distarch: x86_64
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] target_arch: x86_64
2022-10-28T18:47:30.513+0000 I CONTROL [initandlisten] options: { net: { bindIp: "0.0.0.0", port: 27020 }, repair: true, storage: { dbPath: "/data/db" } }
2022-10-28T18:47:30.517+0000 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=1425M,session_max=20000,eviction=(threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),,log=(enabled=false),
2022-10-28T18:47:30.630+0000 I CONTROL [initandlisten]
2022-10-28T18:47:30.630+0000 I CONTROL [initandlisten] ** WARNING: Access control is not enabled for the database.
2022-10-28T18:47:30.630+0000 I CONTROL [initandlisten] ** Read and write access to data and configuration is unrestricted.
2022-10-28T18:47:30.630+0000 I CONTROL [initandlisten] ** WARNING: You are running this process as the root user, which is not recommended.
2022-10-28T18:47:30.630+0000 I CONTROL [initandlisten]
2022-10-28T18:47:30.631+0000 I STORAGE [initandlisten] finished checking dbs
2022-10-28T18:47:30.631+0000 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2022-10-28T18:47:30.631+0000 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-27020.sock
2022-10-28T18:47:30.631+0000 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2022-10-28T18:47:30.631+0000 I STORAGE [initandlisten] WiredTigerKVEngine shutting down
2022-10-28T18:47:30.642+0000 I STORAGE [initandlisten] shutdown: removing fs lock...
2022-10-28T18:47:30.642+0000 I CONTROL [initandlisten] now exiting
2022-10-28T18:47:30.642+0000 I CONTROL [initandlisten] shutting down with code:0
I am unsure if this is a successful repair output or not, but would really appreciate some guidance in next steps or things to check if anyone has seen or dealt with a failure like this before. Any input would be greatly appreciated.
Thank you.