Converting a standalone MongoDB instance to a single-node replica set - mongodb

Question

I am trying to convert my standalone MongoDB instance to a single-node replica set, for the purpose of live migrating to Atlas.
I followed this procedure: https://docs.mongodb.com/manual/tutorial/convert-standalone-to-replica-set/
The step I took were:
$sudo service mongodb stop
$sudo service mongod start
$mongo
>rs.initiate()
{
"info2" : "no configuration explicitly specified -- making one",
"me" : "staging3.domain.io:27017",
"info" : "Config now saved locally. Should come online in about a minute.",
"ok" : 1
}
singleNodeRepl:PRIMARY> rs.status()
{
"set" : "singleNodeRepl",
"date" : ISODate("2020-11-26T00:46:25Z"),
"myState" : 1,
"members" : [
{
"_id" : 0,
"name" : "staging4.domain.io:27017",
"health" : 1,
"state" : 1,
"stateStr" : "PRIMARY",
"uptime" : 1197,
"optime" : Timestamp(1606350415, 1),
"optimeDate" : ISODate("2020-11-26T00:26:55Z"),
"electionTime" : Timestamp(1606350415, 2),
"electionDate" : ISODate("2020-11-26T00:26:55Z"),
"self" : true
}
],
"ok" : 1
}
singleNodeRepl:PRIMARY> db.oplog.rs.find()
{ "ts" : Timestamp(1606350415, 1), "h" : NumberLong(0), "v" : 2, "op" : "n", "ns" : "", "o" : { "msg" : "initiating set" } }
At this point, it seems to have no issues.
However, my application is not being able to work as it did before.
Would really appreciate any help in troubleshooting the issue.
Thank you.
EDIT:
As suggested I included replSet in the config file instead passing it as an argument.
This is my config file:
# mongod.conf
#where to log
logpath=/var/log/mongodb/mongod.log
logappend=true
# fork and run in background
fork=true
#port=27017
dbpath=/var/lib/mongo
# location of pidfile
pidfilepath=/var/run/mongodb/mongod.pid
# Listen to local interface only. Comment out to listen on all interfaces.
#bind_ip=127.0.0.1
# Disables write-ahead journaling
# nojournal=true
# Enables periodic logging of CPU utilization and I/O wait
#cpu=true
# Turn on/off security. Off is currently the default
#noauth=true
#auth=true
# Verbose logging output.
verbose=true
# Inspect all client data for validity on receipt (useful for
# developing drivers)
#objcheck=true
# Enable db quota management
#quota=true
# Set oplogging level where n is
# 0=off (default)
# 1=W
# 2=R
# 3=both
# 7=W+some reads
#diaglog=0
# Ignore query hints
#nohints=true
# Enable the HTTP interface (Defaults to port 28017).
#httpinterface=true
# Turns off server-side scripting. This will result in greatly limited
# functionality
#noscripting=true
# Turns off table scans. Any query that would do a table scan fails.
#notablescan=true
# Disable data file preallocation.
#noprealloc=true
# Specify .ns file size for new databases.
# nssize=<size>
# Replication Options
# in replicated mongo databases, specify the replica set name here
replSet=singleNodeRepl
# maximum size in megabytes for replication operation log
#oplogSize=1024
# path to a key file storing authentication info for connections
# between replica set members
#keyFile=/path/to/keyfile
And verbose log file:
It does look like everything is working fine. However, my application is not able to connect to the DB as it did.
2020-11-26T00:26:55.852+0000 [conn1] replSet replSetInitiate admin command received from client
2020-11-26T00:26:55.853+0000 [conn1] replSet info initiate : no configuration specified. Using a default configuration for the set
2020-11-26T00:26:55.853+0000 [conn1] replSet created this configuration for initiation : { _id: "singleNodeRepl", members: [ { _id: 0, host: "staging4.domain.io:27017" } ] }
2020-11-26T00:26:55.853+0000 [conn1] replSet replSetInitiate config object parses ok, 1 members specified
2020-11-26T00:26:55.853+0000 [conn1] getMyAddrs(): [127.0.0.1] [10.20.26.228] [::1] [fe80::8ed:65ff:fe9e:15ab%eth0]
2020-11-26T00:26:55.853+0000 [conn1] getallIPs("staging4.domain.io"): [127.0.0.1]
2020-11-26T00:26:55.853+0000 [conn1] replSet replSetInitiate all members seem up
2020-11-26T00:26:55.853+0000 [conn1] ******
2020-11-26T00:26:55.853+0000 [conn1] creating replication oplog of size: 2570MB...
2020-11-26T00:26:55.853+0000 [conn1] create collection local.oplog.rs { size: 2695574937.6, capped: true, autoIndexId: false }
2020-11-26T00:26:55.853+0000 [conn1] Database::_addNamespaceToCatalog ns: local.oplog.rs
2020-11-26T00:26:55.866+0000 [conn1] ExtentManager::increaseStorageSize ns:local.oplog.rs desiredSize:2146426624 fromFreeList: 0 eloc: 1:2000
2020-11-26T00:26:55.876+0000 [conn1] ExtentManager::increaseStorageSize ns:local.oplog.rs desiredSize:549148160 fromFreeList: 0 eloc: 2:2000
2020-11-26T00:26:55.878+0000 [conn1] ******
2020-11-26T00:26:55.878+0000 [conn1] replSet info saving a newer config version to local.system.replset: { _id: "singleNodeRepl", version: 1, members: [ { _id: 0, host: "staging4.domain.io:27017" } ] }
2020-11-26T00:26:55.878+0000 [conn1] Database::_addNamespaceToCatalog ns: local.system.replset
2020-11-26T00:26:55.878+0000 [conn1] ExtentManager::increaseStorageSize ns:local.system.replset desiredSize:8192 fromFreeList: 0 eloc: 2:20bb8000
2020-11-26T00:26:55.878+0000 [conn1] Database::_addNamespaceToCatalog ns: local.system.replset.$_id_
2020-11-26T00:26:55.878+0000 [conn1] build index on: local.system.replset properties: { v: 1, key: { _id: 1 }, name: "_id_", ns: "local.system.replset" }
2020-11-26T00:26:55.878+0000 [conn1] local.system.replset: clearing plan cache - collection info cache reset
2020-11-26T00:26:55.878+0000 [conn1] allocating new extent
2020-11-26T00:26:55.878+0000 [conn1] ExtentManager::increaseStorageSize ns:local.system.replset.$_id_ desiredSize:131072 fromFreeList: 0 eloc: 2:20bba000
2020-11-26T00:26:55.878+0000 [conn1] added index to empty collection
2020-11-26T00:26:55.878+0000 [conn1] local.system.replset: clearing plan cache - collection info cache reset
2020-11-26T00:26:55.878+0000 [conn1] replSet saveConfigLocally done
2020-11-26T00:26:55.878+0000 [conn1] replSet replSetInitiate config now saved locally. Should come online in about a minute.
2020-11-26T00:26:55.878+0000 [conn1] command admin.$cmd command: replSetInitiate { replSetInitiate: undefined } keyUpdates:0 numYields:0 locks(micros) W:25362 reslen:206 25ms
2020-11-26T00:26:55.879+0000 [conn1] command test.$cmd command: isMaster { isMaster: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:270 0ms
2020-11-26T00:27:01.256+0000 [conn1] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:27:01.257+0000 [conn1] command test.$cmd command: isMaster { isMaster: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:367 0ms
2020-11-26T00:27:10.688+0000 [conn1] query local.system.replset planSummary: COLLSCAN ntoskip:0 nscanned:1 nscannedObjects:1 keyUpdates:0 numYields:0 locks(micros) r:97 nreturned:1 reslen:126 0ms
2020-11-26T00:27:10.689+0000 [conn1] command test.$cmd command: isMaster { isMaster: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:367 0ms
2020-11-26T00:27:28.889+0000 [clientcursormon] connections:1
2020-11-26T00:27:33.333+0000 [conn1] end connection 127.0.0.1:50580 (0 connections now open)
2020-11-26T00:27:57.230+0000 [initandlisten] connection accepted from 127.0.0.1:50582 #2 (1 connection now open)
2020-11-26T00:27:57.230+0000 [conn2] command admin.$cmd command: whatsmyuri { whatsmyuri: 1 } ntoreturn:1 keyUpdates:0 numYields:0 reslen:62 0ms
2020-11-26T00:27:57.232+0000 [conn2] command admin.$cmd command: getLog { getLog: "startupWarnings" } keyUpdates:0 numYields:0 reslen:70 0ms
2020-11-26T00:27:57.233+0000 [conn2] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:28:00.237+0000 [conn2] command admin.$cmd command: serverStatus { serverStatus: 1.0 } keyUpdates:0 numYields:0 locks(micros) r:13 reslen:3402 0ms
2020-11-26T00:28:00.242+0000 [conn2] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:28:16.560+0000 [conn2] end connection 127.0.0.1:50582 (0 connections now open)
2020-11-26T00:32:28.904+0000 [clientcursormon] connections:0
2020-11-26T00:36:32.398+0000 [initandlisten] connection accepted from 127.0.0.1:50588 #3 (1 connection now open)
2020-11-26T00:36:32.398+0000 [conn3] command admin.$cmd command: whatsmyuri { whatsmyuri: 1 } ntoreturn:1 keyUpdates:0 numYields:0 reslen:62 0ms
2020-11-26T00:36:32.399+0000 [conn3] command admin.$cmd command: getLog { getLog: "startupWarnings" } keyUpdates:0 numYields:0 reslen:70 0ms
2020-11-26T00:36:32.400+0000 [conn3] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:36:34.603+0000 [conn3] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:36:37.326+0000 [conn3] query local.oplog.rs planSummary: COLLSCAN ntoreturn:0 ntoskip:0 nscanned:1 nscannedObjects:1 keyUpdates:0 numYields:0 locks(micros) r:66 nreturned:1 reslen:106 0ms
2020-11-26T00:36:37.328+0000 [conn3] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:37:28.832+0000 [initandlisten] connection accepted from 10.20.37.160:54484 #4 (2 connections now open)
2020-11-26T00:37:28.832+0000 [conn4] command admin.$cmd command: isMaster { isMaster: 1, compression: [], client: { driver: { name: "mongo-ruby-driver", version: "2.13.1" }, os: { type: "linux", name: "linux-gnu", architecture: "x86_64" }, platform: "mongoid-6.4.1, Ruby 2.6.5, x86_64-linux, x86_64-pc-linux-gnu" } } keyUpdates:0 numYields:0 reslen:367 0ms
2020-11-26T00:37:28.919+0000 [clientcursormon] connections:2
2020-11-26T00:37:33.568+0000 [initandlisten] connection accepted from 10.20.37.160:54492 #5 (3 connections now open)
2020-11-26T00:37:33.569+0000 [conn5] command admin.$cmd command: isMaster { isMaster: 1, compression: [], client: { driver: { name: "mongo-ruby-driver", version: "2.13.1" }, os: { type: "linux", name: "linux-gnu", architecture: "x86_64" }, platform: "mongoid-6.4.1, Ruby 2.6.5, x86_64-linux, x86_64-pc-linux-gnu" } } keyUpdates:0 numYields:0 reslen:367 0ms
2020-11-26T00:37:36.586+0000 [conn3] end connection 127.0.0.1:50588 (2 connections now open)
2020-11-26T00:39:35.621+0000 [initandlisten] connection accepted from 127.0.0.1:50592 #6 (3 connections now open)
2020-11-26T00:39:35.621+0000 [conn6] command admin.$cmd command: whatsmyuri { whatsmyuri: 1 } ntoreturn:1 keyUpdates:0 numYields:0 reslen:62 0ms
2020-11-26T00:39:35.622+0000 [conn6] command admin.$cmd command: getLog { getLog: "startupWarnings" } keyUpdates:0 numYields:0 reslen:70 0ms
2020-11-26T00:39:35.623+0000 [conn6] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:39:37.589+0000 [conn6] opening db: test
2020-11-26T00:39:37.589+0000 [conn6] query test.oplog.rs planSummary: EOF ntoreturn:0 ntoskip:0 nscanned:0 nscannedObjects:0 keyUpdates:0 numYields:0 locks(micros) W:186 r:19 nreturned:0 reslen:20 0ms
2020-11-26T00:39:37.590+0000 [conn6] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:39:41.891+0000 [conn6] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:39:43.266+0000 [conn6] query local.oplog.rs planSummary: COLLSCAN ntoreturn:0 ntoskip:0 nscanned:1 nscannedObjects:1 keyUpdates:0 numYields:0 locks(micros) r:62 nreturned:1 reslen:106 0ms
2020-11-26T00:39:43.268+0000 [conn6] command admin.$cmd command: replSetGetStatus { replSetGetStatus: 1.0, forShell: 1.0 } keyUpdates:0 numYields:0 reslen:300 0ms
2020-11-26T00:39:52.681+0000 [conn6] end connection 127.0.0.1:50592 (2 connections now open)
2020-11-26T00:42:28.934+0000 [clientcursormon] connections:2

Answer 1

You should not mix using a config file, i.e.
mongod --config /etc/mongod.conf
and command line options
mongod --replSet rs0 --bind_ip localhost
Most likely in your config you did not set in /etc/mongod.conf
replication:
replSetName: <string>
So, when you start your MongoDB with service mongodb start then you may have a different configuration.
Note, check the service file (in my Redhat at /etc/systemd/system/mongod.service) which may point even to a different .conf file.