MongoDB not starting in docker-compose but mongod.service does work - mongodb

Question

I am developing some application with a MongoDB database, a Nestjs API and front-end in Angular.
Currently, we develop stuff locally then deploy it on a CentOS-based VM. To that end, we put everything inside a docker-compose.
However, although mongodb is in the "general" docker-compose, it has been running in a separate compose up to now.
My problem arose while trying to update the VM with our newest developments.
I used docker-compose down to turn down the mongod service, then wanted to run our other compose to upgrade the application.
However, mongodb failed and returned error code = 14. And now I can't launch it back from the dedicated docker-compose.
However, I am still able to repair the mongodb.service and access my database by using :
chown -R mongod:mongod /var/lib/mongo/
chown mongod:mongod /tmp/mongodb-27017.sock
systemctl start mongod
What could be the problem here??
Here is the docker-compose file. From what I understand, it uses an image of MongoDB already built, so I do not have a Dockerfile.
version: '3.3'
services:
# API
#nestjs:
#container_name: nestjs_dev
#image: nestjs-api:1.0.0
#command: npm run start:prod
# Default port
#ports:
#- 8080:8080
#networks:
#- nestjs-network
#depends_on:
#- mongodb
#restart: always
# Database
mongodb:
image: mongo:latest
container_name: mongodb
volumes:
- /etc/mongod.conf:/etc/mongod.conf:z
- /var/lib/mongo:/data/db:z
# Default port
ports:
- 27017:27017
networks:
- nestjs-network
#restart: always
networks:
nestjs-network:
Finally, I noticed that there is a 1-hour difference between "real" time, and the time in the log produced when trying to docker-compose up :
Notice the 1-hour delta
I was expecting the docker-compose to run mongod normally, as it always did.
Instead, mongod returned error code 14.
I tried the chown commands, changing the mongod.conf file, etc. Ultimately, I think it is an issue with my compose.
Edit : Here is the log from the docker-compose :
2023-02-19T17:42:05.031063000Z {"t":{"$date":"2023-02-19T17:42:05.029+00:00"},"s":"I", "c":"CONTROL", "id":23285, "ctx":"-","msg":"Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'"}
2023-02-19T17:42:05.031365000Z {"t":{"$date":"2023-02-19T17:42:05.030+00:00"},"s":"I", "c":"NETWORK", "id":4915701, "ctx":"main","msg":"Initialized wire specification","attr":{"spec":{"incomingExternalClient":{"minWireVersion":0,"maxWireVersion":17},"incomingInternalClient":{"minWireVersion":0,"maxWireVersion":17},"outgoing":{"minWireVersion":6,"maxWireVersion":17},"isInternalClient":true}}}
2023-02-19T17:42:05.031583000Z {"t":{"$date":"2023-02-19T17:42:05.031+00:00"},"s":"I", "c":"NETWORK", "id":4648601, "ctx":"main","msg":"Implicit TCP FastOpen unavailable. If TCP FastOpen is required, set tcpFastOpenServer, tcpFastOpenClient, and tcpFastOpenQueueSize."}
2023-02-19T17:42:05.033237000Z {"t":{"$date":"2023-02-19T17:42:05.032+00:00"},"s":"I", "c":"REPL", "id":5123008, "ctx":"main","msg":"Successfully registered PrimaryOnlyService","attr":{"service":"TenantMigrationDonorService","namespace":"config.tenantMigrationDonors"}}
2023-02-19T17:42:05.033460000Z {"t":{"$date":"2023-02-19T17:42:05.032+00:00"},"s":"I", "c":"REPL", "id":5123008, "ctx":"main","msg":"Successfully registered PrimaryOnlyService","attr":{"service":"TenantMigrationRecipientService","namespace":"config.tenantMigrationRecipients"}}
2023-02-19T17:42:05.033665000Z {"t":{"$date":"2023-02-19T17:42:05.032+00:00"},"s":"I", "c":"REPL", "id":5123008, "ctx":"main","msg":"Successfully registered PrimaryOnlyService","attr":{"service":"ShardSplitDonorService","namespace":"config.tenantSplitDonors"}}
2023-02-19T17:42:05.033865000Z {"t":{"$date":"2023-02-19T17:42:05.032+00:00"},"s":"I", "c":"CONTROL", "id":5945603, "ctx":"main","msg":"Multi threading initialized"}
2023-02-19T17:42:05.034102000Z {"t":{"$date":"2023-02-19T17:42:05.033+00:00"},"s":"F", "c":"CONTROL", "id":6384300, "ctx":"main","msg":"Writing fatal message","attr":{"message":"terminate() called. An exception is active; attempting to gather more information\n"}}
2023-02-19T17:42:05.034424000Z {"t":{"$date":"2023-02-19T17:42:05.033+00:00"},"s":"F", "c":"CONTROL", "id":6384300, "ctx":"main","msg":"Writing fatal message","attr":{"message":"std::exception::what(): Operation not permitted\nActual exception type: std::system_error\n\n"}}
2023-02-19T17:42:05.168487000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31380, "ctx":"main","msg":"BACKTRACE","attr":{"bt":{"backtrace":[{"a":"555603E458D4","b":"5555FF067000","o":"4DDE8D4","s":"_ZN5mongo18stack_trace_detail12_GLOBAL__N_119printStackTraceImplERKNS1_7OptionsEPNS_14StackTraceSinkE.constprop.362","C":"mongo::stack_trace_detail::(anonymous namespace)::printStackTraceImpl(mongo::stack_trace_detail::(anonymous namespace)::Options const&, mongo::StackTraceSink*) [clone .constprop.362]","s+":"1F4"},{"a":"555603E47E19","b":"5555FF067000","o":"4DE0E19","s":"_ZN5mongo15printStackTraceEv","C":"mongo::printStackTrace()","s+":"29"},{"a":"555603E42167","b":"5555FF067000","o":"4DDB167","s":"_ZN5mongo12_GLOBAL__N_111myTerminateEv","C":"mongo::(anonymous namespace)::myTerminate()","s+":"D7"},{"a":"555603FCCBF6","b":"5555FF067000","o":"4F65BF6","s":"_ZN10__cxxabiv111__terminateEPFvvE","C":"__cxxabiv1::__terminate(void (*)())","s+":"6"},{"a":"555603FCCC31","b":"5555FF067000","o":"4F65C31","s":"_ZSt9terminatev","C":"std::terminate()","s+":"11"},{"a":"555603FCCD6B","b":"5555FF067000","o":"4F65D6B","s":"__cxa_throw","s+":"4B"},{"a":"555600F7647B","b":"5555FF067000","o":"1F0F47B","s":"_ZSt20__throw_system_errori.cold.24","C":"std::__throw_system_error(int) [clone .cold.24]","s+":"2F"},{"a":"555603FE8F69","b":"5555FF067000","o":"4F81F69","s":"_ZNSt6thread15_M_start_threadESt10unique_ptrINS_6_StateESt14default_deleteIS1_EEPFvvE","C":"std::thread::_M_start_thread(std::unique_ptr<std::thread::_State, std::default_delete<std::thread::_State> >, void (*)())","s+":"29"},{"a":"555601F1107A","b":"5555FF067000","o":"2EAA07A","s":"_ZN5mongo27startSignalProcessingThreadENS_13LogFileStatusE","C":"mongo::startSignalProcessingThread(mongo::LogFileStatus)","s+":"11A"},{"a":"5556011871EA","b":"5555FF067000","o":"21201EA","s":"_ZN5mongo11mongod_mainEiPPc","C":"mongo::mongod_main(int, char**)","s+":"B8A"},{"a":"555600F771BE","b":"5555FF067000","o":"1F101BE","s":"main","s+":"E"},{"a":"7F9113BC8D90","b":"7F9113B9F000","o":"29D90","s":"__libc_init_first","s+":"90"},{"a":"7F9113BC8E40","b":"7F9113B9F000","o":"29E40","s":"__libc_start_main","s+":"80"},{"a":"555601181A95","b":"5555FF067000","o":"211AA95","s":"_start","s+":"25"}],"processInfo":{"mongodbVersion":"6.0.4","gitVersion":"44ff59461c1353638a71e710f385a566bcd2f547","compiledModules":[],"uname":{"sysname":"Linux","release":"3.10.0-1160.83.1.el7.x86_64","version":"#1 SMP Wed Jan 25 16:41:43 UTC 2023","machine":"x86_64"},"somap":[{"b":"5555FF067000","elfType":3,"buildId":"BCB8F6C3AD4ABF41C81882BAE25C6885C6266CC4"},{"b":"7F9113B9F000","path":"/lib/x86_64-linux-gnu/libc.so.6","elfType":3,"buildId":"69389D485A9793DBE873F0EA2C93E02EFAA9AA3D"}]}}},"tags":[]}
2023-02-19T17:42:05.171495000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603E458D4","b":"5555FF067000","o":"4DDE8D4","s":"_ZN5mongo18stack_trace_detail12_GLOBAL__N_119printStackTraceImplERKNS1_7OptionsEPNS_14StackTraceSinkE.constprop.362","C":"mongo::stack_trace_detail::(anonymous namespace)::printStackTraceImpl(mongo::stack_trace_detail::(anonymous namespace)::Options const&, mongo::StackTraceSink*) [clone .constprop.362]","s+":"1F4"}}}
2023-02-19T17:42:05.172869000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603E47E19","b":"5555FF067000","o":"4DE0E19","s":"_ZN5mongo15printStackTraceEv","C":"mongo::printStackTrace()","s+":"29"}}}
2023-02-19T17:42:05.173129000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603E42167","b":"5555FF067000","o":"4DDB167","s":"_ZN5mongo12_GLOBAL__N_111myTerminateEv","C":"mongo::(anonymous namespace)::myTerminate()","s+":"D7"}}}
2023-02-19T17:42:05.173356000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603FCCBF6","b":"5555FF067000","o":"4F65BF6","s":"_ZN10__cxxabiv111__terminateEPFvvE","C":"__cxxabiv1::__terminate(void (*)())","s+":"6"}}}
2023-02-19T17:42:05.173565000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603FCCC31","b":"5555FF067000","o":"4F65C31","s":"_ZSt9terminatev","C":"std::terminate()","s+":"11"}}}
2023-02-19T17:42:05.173769000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603FCCD6B","b":"5555FF067000","o":"4F65D6B","s":"__cxa_throw","s+":"4B"}}}
2023-02-19T17:42:05.173997000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555600F7647B","b":"5555FF067000","o":"1F0F47B","s":"_ZSt20__throw_system_errori.cold.24","C":"std::__throw_system_error(int) [clone .cold.24]","s+":"2F"}}}
2023-02-19T17:42:05.174219000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555603FE8F69","b":"5555FF067000","o":"4F81F69","s":"_ZNSt6thread15_M_start_threadESt10unique_ptrINS_6_StateESt14default_deleteIS1_EEPFvvE","C":"std::thread::_M_start_thread(std::unique_ptr<std::thread::_State, std::default_delete<std::thread::_State> >, void (*)())","s+":"29"}}}
2023-02-19T17:42:05.174451000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555601F1107A","b":"5555FF067000","o":"2EAA07A","s":"_ZN5mongo27startSignalProcessingThreadENS_13LogFileStatusE","C":"mongo::startSignalProcessingThread(mongo::LogFileStatus)","s+":"11A"}}}
2023-02-19T17:42:05.174675000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"5556011871EA","b":"5555FF067000","o":"21201EA","s":"_ZN5mongo11mongod_mainEiPPc","C":"mongo::mongod_main(int, char**)","s+":"B8A"}}}
2023-02-19T17:42:05.174881000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555600F771BE","b":"5555FF067000","o":"1F101BE","s":"main","s+":"E"}}}
2023-02-19T17:42:05.175099000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"7F9113BC8D90","b":"7F9113B9F000","o":"29D90","s":"__libc_init_first","s+":"90"}}}
2023-02-19T17:42:05.175328000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"7F9113BC8E40","b":"7F9113B9F000","o":"29E40","s":"__libc_start_main","s+":"80"}}}
2023-02-19T17:42:05.175540000Z {"t":{"$date":"2023-02-19T17:42:05.167+00:00"},"s":"I", "c":"CONTROL", "id":31445, "ctx":"main","msg":"Frame","attr":{"frame":{"a":"555601181A95","b":"5555FF067000","o":"211AA95","s":"_start","s+":"25"}}}