MongoDB has very similar features with RDBMS database. Like any other DB, it can be shutdown and started up for example:

You can start MongoDB from a file as follows:

[root@tain-cx-mdb1 scripts]# ./startMongoDB.sh
about to fork child process, waiting until server is ready for connections.
forked process: 67867
child process started successfully, parent exiting

Where the script contains:

startMongoDB

#!/bin/bash
sudo /bin/mongod --auth -f /app/mongo/hunterServer/conf/mongo.conf --fork

and the contents of the configuration file is:

mongo.conf

port = 9005
logpath = /var/mongodb/logs/mongodb.log
logappend = true
pidfilepath = /var/mongodb/run/mongodb.pid
unixSocketPrefix = /var/mongodb/db
dbpath = /var/mongodb/db
smallfiles = true
maxConns = 16000

The database can also be shutdown as follows:

~/mongodb/bin/mongo localhost:9005/admin --eval "db.shutdownServer()"

or you can do it manually using

mongo admin -u  'adminDBA' -p 'password' --port 9005 --eval "db.shutdownServer()"

The shell can be set to more readable manner as follows:

prompt = function() {
    user = db.runCommand({connectionStatus:1}).authInfo.authenticatedUsers[0]
    host = db.getMongo().toString().split(" ")[2]
    curDB = db.getName()
    if (user) {
       uname = user.user
    }
    else {
       uname = "local"
    }
    return uname + "@" + host + ":" + curDB + "> "
}

[email protected]:9005:admin>
[email protected]:9005:admin>
[email protected]:9005:admin>
   ^         ^       ^    ^
   |         |       |    |
Username IP Address Port Database

From 4.2 the: MMAPv1 is depricated, so if you are thinking of upgrading to 4.2, we have to change the storage engine. The engine isn't easy though. In nutshell we should:

1. Perform export
2. Create new directory for that storage engine (mongo should have read/write).
3. Edit the mongo configuration file to use the new folder and storage engine.
4. Restart the mongo with that storage engine.
5. Restore the export.

The export can be done wherever you can, in our case we will create a new directory for that backup:

[root@localhost mongo]# mkdir -p /app/data/mongo
[root@localhost mongo]# cd /app/data
[root@localhost data]# ls -alrt
total 0
drwxr-xr-x. 2 root root  6 Sep 10 15:20 mongo
drwxr-xr-x. 3 root root 18 Sep 10 15:20 ..
drwxr-xr-x. 3 root root 19 Sep 10 15:20 .
[root@localhost data]# mkdir backup
[root@localhost data]# cd backup/
[root@localhost data]# ls -alrt
total 0
drwxr-xr-x. 2 root root  6 Sep 10 15:20 mongo <- Our new database folder with WIREDTIGER
drwxr-xr-x. 3 root root 18 Sep 10 15:20 ..
drwxr-xr-x. 4 root root 33 Sep 10 15:22 .
drwxr-xr-x. 6 root root 62 Sep 10 15:25 backup <- The backup (export) location

The export is done very easy:

 
[root@localhost backup]# mongodump  --out /app/data/backup -u adminDBA -p password123 --authenticationDatabase admin
2019-09-10T15:25:28.642-0400    writing admin.system.indexes to
2019-09-10T15:25:28.649-0400    done dumping admin.system.indexes (4 documents)
2019-09-10T15:25:28.649-0400    writing config.system.indexes to
2019-09-10T15:25:28.656-0400    done dumping config.system.indexes (2 documents)
2019-09-10T15:25:28.656-0400    writing admin.system.users to
2019-09-10T15:25:28.663-0400    done dumping admin.system.users (1 document)
2019-09-10T15:25:28.663-0400    writing admin.system.version to
2019-09-10T15:25:28.671-0400    done dumping admin.system.version (2 documents)
2019-09-10T15:25:28.671-0400    writing test.mycol1 to
2019-09-10T15:25:28.671-0400    writing ExampleDB.ExampleCol to
2019-09-10T15:25:28.691-0400    done dumping ExampleDB.ExampleCol (2 documents)
2019-09-10T15:25:28.691-0400    done dumping test.mycol1 (20 documents)

We have to modify the config file so it will point to the new folder and with the correct engine:

# Where and how to store data.
storage:
  dbPath: /app/data/mongo <- The New folder
  journal:
    enabled: true
  engine: wiredTiger <- The New engine

P.S. Disable the authentication for now, since it will be problem later:

security:
  authorization: "disabled"

Feel free to restart the mongo however you want :)

[root@localhost mongo]# mongo -u adminDBA -p password123 localhost:27017/admin --eval "db.shutdownServer()"
MongoDB shell version v4.0.12
connecting to: mongodb://localhost:27017/admin?gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("a3cdb4ff-b70b-4107-af33-c180dd186669") }
MongoDB server version: 4.0.12
2019-09-10T15:30:00.110-0400 I NETWORK  [js] DBClientConnection failed to receive message from localhost:27017 - HostUnreachable: Connection closed by peer
server should be down...
2019-09-10T15:30:00.113-0400 I NETWORK  [js] trying reconnect to localhost:27017 failed
2019-09-10T15:30:00.113-0400 I NETWORK  [js] reconnect localhost:27017 failed failed
2019-09-10T15:30:00.113-0400 I QUERY    [js] Failed to end session { id: UUID("a3cdb4ff-b70b-4107-af33-c180dd186669") } due to SocketException: socket exception [CONNECT_ERROR] server [couldn't connect to server localhost:27017, connection attempt failed: SocketException: Error connecting to localhost:27017 (127.0.0.1:27017) :: caused by :: Connection refused]
[root@localhost mongo]# ps -ef | grep mongo
root      6360  4437  0 15:30 pts/1    00:00:00 grep --color=auto mongo

[root@localhost mongo]# /bin/mongod -f /etc/mongod.conf --fork
2019-09-10T15:32:49.796-0400 I STORAGE  [main] Max cache overflow file size custom option: 0
about to fork child process, waiting until server is ready for connections.
forked process: 6433
child process started successfully, parent exiting
[root@localhost mongo]#
[root@localhost mongo]#
[root@localhost mongo]# mongo
MongoDB shell version v4.0.12
connecting to: mongodb://127.0.0.1:27017/?gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("8f22cb0d-f851-4e78-9483-d58f479c4e4f") }
MongoDB server version: 4.0.12
Server has startup warnings:
2019-09-10T15:32:50.560-0400 I CONTROL  [initandlisten] ** WARNING: You are running this process as the root user, which is not recommended.
2019-09-10T15:32:50.560-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
---
Enable MongoDB's free cloud-based monitoring service, which will then receive and display
metrics about your deployment (disk utilization, CPU, operation statistics, etc).

The monitoring data will be available on a MongoDB website with a unique URL accessible to you
and anyone you share the URL with. MongoDB may use this information to make product
improvements and to suggest MongoDB products and deployment options to you.

To enable free monitoring, run the following command: db.enableFreeMonitoring()
To permanently disable this reminder, run the following command: db.disableFreeMonitoring()
---

> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB
>
bye

If the authentication isn't disabled, that will create a problem since in the config file the authentication is enabled, but the user (which is in the admin database in our case) cannot be used. So ensure the authentication is disabled:

[root@localhost mongo]# mongorestore /app/data/backup/
2019-09-10T15:33:08.051-0400    preparing collections to restore from
2019-09-10T15:33:08.059-0400    reading metadata for test.mycol1 from /app/data/backup/test/mycol1.metadata.json
2019-09-10T15:33:08.060-0400    reading metadata for ExampleDB.ExampleCol from /app/data/backup/ExampleDB/ExampleCol.metadata.json
2019-09-10T15:33:08.087-0400    restoring test.mycol1 from /app/data/backup/test/mycol1.bson
2019-09-10T15:33:08.105-0400    no indexes to restore
2019-09-10T15:33:08.105-0400    finished restoring test.mycol1 (20 documents)
2019-09-10T15:33:08.123-0400    restoring ExampleDB.ExampleCol from /app/data/backup/ExampleDB/ExampleCol.bson
2019-09-10T15:33:08.125-0400    no indexes to restore
2019-09-10T15:33:08.125-0400    finished restoring ExampleDB.ExampleCol (2 documents)
2019-09-10T15:33:08.125-0400    restoring users from /app/data/backup/admin/system.users.bson
2019-09-10T15:33:08.185-0400    done

We can verify the data, for some reason mongo was showing me 0000, even though there was data in the databases:

[root@localhost mongo]# mongo
MongoDB shell version v4.0.12
connecting to: mongodb://127.0.0.1:27017/?gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("dd544d99-2d70-4c83-8f77-487f9eac0beb") }
MongoDB server version: 4.0.12
Server has startup warnings:
2019-09-10T15:32:50.560-0400 I CONTROL  [initandlisten] ** WARNING: You are running this process as the root user, which is not recommended.
2019-09-10T15:32:50.560-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-09-10T15:32:50.561-0400 I CONTROL  [initandlisten]
---
Enable MongoDB's free cloud-based monitoring service, which will then receive and display
metrics about your deployment (disk utilization, CPU, operation statistics, etc).

The monitoring data will be available on a MongoDB website with a unique URL accessible to you
and anyone you share the URL with. MongoDB may use this information to make product
improvements and to suggest MongoDB products and deployment options to you.

To enable free monitoring, run the following command: db.enableFreeMonitoring()
To permanently disable this reminder, run the following command: db.disableFreeMonitoring()
---

> show dbs
ExampleDB  0.000GB ??
admin      0.000GB ??
config     0.000GB ??
local      0.000GB ??
test       0.000GB ??
> use test
switched to db test
> show collections
mycol1
> db.mycol1.find()
{ "_id" : ObjectId("5d00f49466f8aff37eced4b5"), "count" : 1, "username" : "user1", "password" : "qeg3amrt3xr", "createdOn" : ISODate("2019-06-12T12:48:20.255Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4b6"), "count" : 2, "username" : "user2", "password" : "jxucw3wstt9", "createdOn" : ISODate("2019-06-12T12:48:20.257Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4b7"), "count" : 3, "username" : "user3", "password" : "7r5u24ndn29", "createdOn" : ISODate("2019-06-12T12:48:20.257Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4b8"), "count" : 4, "username" : "user4", "password" : "8o1s4qjjor", "createdOn" : ISODate("2019-06-12T12:48:20.258Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4b9"), "count" : 5, "username" : "user5", "password" : "fyzxovtpgb9", "createdOn" : ISODate("2019-06-12T12:48:20.259Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4ba"), "count" : 6, "username" : "user6", "password" : "k5agz7u8fr", "createdOn" : ISODate("2019-06-12T12:48:20.259Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4bb"), "count" : 7, "username" : "user7", "password" : "5pzn3njnhfr", "createdOn" : ISODate("2019-06-12T12:48:20.260Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4bc"), "count" : 8, "username" : "user8", "password" : "1gxa5szia4i", "createdOn" : ISODate("2019-06-12T12:48:20.261Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4bd"), "count" : 9, "username" : "user9", "password" : "7d6ceyojemi", "createdOn" : ISODate("2019-06-12T12:48:20.263Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f49466f8aff37eced4be"), "count" : 10, "username" : "user10", "password" : "29ix622zkt9", "createdOn" : ISODate("2019-06-12T12:48:20.263Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d675395"), "count" : 1, "username" : "user1", "password" : "8uhzykqpvi", "createdOn" : ISODate("2019-06-12T12:54:52.374Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d675396"), "count" : 2, "username" : "user2", "password" : "zm7v1zcl3di", "createdOn" : ISODate("2019-06-12T12:54:52.374Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d675397"), "count" : 3, "username" : "user3", "password" : "lk3hn597ldi", "createdOn" : ISODate("2019-06-12T12:54:52.375Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d675398"), "count" : 4, "username" : "user4", "password" : "6akj6mvx6r", "createdOn" : ISODate("2019-06-12T12:54:52.375Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d675399"), "count" : 5, "username" : "user5", "password" : "qvj2nyx2yb9", "createdOn" : ISODate("2019-06-12T12:54:52.375Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d67539a"), "count" : 6, "username" : "user6", "password" : "5o9w6zuxr", "createdOn" : ISODate("2019-06-12T12:54:52.376Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d67539b"), "count" : 7, "username" : "user7", "password" : "z2if1rlik9", "createdOn" : ISODate("2019-06-12T12:54:52.377Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d67539c"), "count" : 8, "username" : "user8", "password" : "uyrhvqxs9k9", "createdOn" : ISODate("2019-06-12T12:54:52.377Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d67539d"), "count" : 9, "username" : "user9", "password" : "u2ff0kvs4i", "createdOn" : ISODate("2019-06-12T12:54:52.378Z"), "score" : 0 }
{ "_id" : ObjectId("5d00f61c4422539b4d67539e"), "count" : 10, "username" : "user10", "password" : "a7ny85xw29", "createdOn" : ISODate("2019-06-12T12:54:52.379Z"), "score" : 0 }

The storage and memory can be overviewed as follows:

Server status will give you some rough overview of how the memory is allocated:

> db.serverStatus().mem
{ "bits" : 64, "resident" : 27, "virtual" : 397, "supported" : true }

> db.serverStatus().tcmalloc
... not easy to read! ...
var mem = db.serverStatus().tcmalloc;

mem.tcmalloc.formattedString
> db.serverStatus().tcmalloc.tcmalloc.formattedString
"------------------------------------------------
MALLOC:     2763280920 ( 2635.3 MiB) Bytes in use by application
MALLOC: +    949514240 (  905.5 MiB) Bytes in page heap freelist
MALLOC: +    135775296 (  129.5 MiB) Bytes in central cache freelist
MALLOC: +      2762912 (    2.6 MiB) Bytes in transfer cache freelist
MALLOC: +     42041608 (   40.1 MiB) Bytes in thread cache freelists
MALLOC: +     16965888 (   16.2 MiB) Bytes in malloc metadata
MALLOC:   ------------
MALLOC: =   3910340864 ( 3729.2 MiB) Actual memory used (physical + swap)
MALLOC: +    147517440 (  140.7 MiB) Bytes released to OS (aka unmapped)
MALLOC:   ------------
MALLOC: =   4057858304 ( 3869.9 MiB) Virtual address space used
MALLOC:
MALLOC:          62521              Spans in use
MALLOC:             78              Thread heaps in use
MALLOC:           4096              Tcmalloc page size
------------------------------------------------
Call ReleaseFreeMemory() to release freelist memory to the OS (via madvise()).
Bytes released to the OS take up virtual address space but no physical memory.

So you can see how much memory your database is storing.

The storage can be checked as follows:

> db.getCollectionNames().map(name => ({totalIndexSize: db.getCollection(name).stats().totalIndexSize, name: name})).sort((a, b) => a.totalIndexSize - b.totalIndexSize).forEach(printjson)

{ "totalIndexSize" : 69632, "name" : "dealers" }
{ "totalIndexSize" : 69632, "name" : "users" }
{ "totalIndexSize" : 73728, "name" : "authorization.permissions" }
{ "totalIndexSize" : 73728, "name" : "authorization.roles" }
{ "totalIndexSize" : 73728, "name" : "authorization.rules" }
{ "totalIndexSize" : 221184, "name" : "procedures" }
{ "totalIndexSize" : 372736, "name" : "reviews" }
{ "totalIndexSize" : 856064, "name" : "violations" }
{ "totalIndexSize" : 1617920, "name" : "incidents" }
{ "totalIndexSize" : 2031616, "name" : "files.files" }
{ "totalIndexSize" : 2732032, "name" : "rounds.requests" }
{ "totalIndexSize" : 23449600, "name" : "files.chunks" }
{ "totalIndexSize" : 114831360, "name" : "audit.trails" }
{ "totalIndexSize" : 368611328, "name" : "rounds" }

Of course you can investigate it further with:

> db.rounds.stats().indexSizes
{
        "_id_" : 64692224,
        "rounds_unique" : 58056704,
        "rounds_sort_dealer_name" : 18669568,
        "rounds_sort_is_closed" : 17887232,
        "rounds_sort_video_id" : 18415616,
        "rounds_sort_started_at" : 55402496,
        "rounds_text_game_code" : 113971200,
        "rounds_sort_is_cancelled" : 21516288
}
>

var collectionNames = db.getCollectionNames(), stats = [];
collectionNames.forEach(function (n) { stats.push(db[n].stats()); });
for (var c in stats) {
    print(stats[c]['ns'] + ": " + stats[c]['size'] + " (" + stats[c]['storageSize'] + ")");
}

var collectionNames = db.getCollectionNames()
var col_stats = [];

// Get stats for every collections
collectionNames.forEach(function (n) { 
    col_stats.push(db.getCollection(n).stats());
});

// Print
for (var item of col_stats) {
    print(`${item['ns']} | size: ${item['size']} 
(${(item['size']/1073741824).toFixed(2)} GB) | storageSize: ${item['storageSize']} 
(${(item['storageSize']/1073741824).toFixed(2)} GB)`);
}

Data in Mongo Database can easily become fragmented. Especially with frequent additions and removals. Let's check one example:

> db.files.chunks.stats()
{
        "ns" : "incident.files.chunks",
        "size" : 148870322967,
        "count" : 588516,
        "avgObjSize" : 252958,
        "storageSize" : 394018263040,
        "capped" : false,
        "wiredTiger" : {....}

On our example, this collection “file.chunks” is 148870322967 bytes in data but it occupies 394018263040 on disk level. In other words the data is more than 100% fragmented.

In order to defremant a collection we have two options, depending on the storage engine:

• MMAPv1 : Repair a whole database or directory location
• WiredTiger: Compact Collection.

Let's see how this is done in each of them:

If your storage engine is MMAPv1, this is your way forward. The repairDatabase command is used for checking and repairing errors and inconsistencies in your data. It performs a rewrite of your data, freeing up any unused disk space along with it. Like compact, it will block all other operations on your database. Running repairDatabase can take a lot of time depending on the amount of data in your db, and it will also completely remove any corrupted data it finds.

mongod --repair --repairpath /mnt/vol1

db.repairDatabase()

or

db.runCommand({repairDatabase:1})

RepairDatabase needs free space equivalent to the data in your database and an additional 2GB more. It can be run either from the system shell or from within the mongo shell. Depending on the amount of data you have, it may be necessary to assign a sperate volume for this using the –repairpath option.

he compact command works at the collection level, so each collection in your database will have to be compacted one by one. This completely rewrites the data and indexes to remove fragmentation. In addition, if your storage engine is WiredTiger, the compact command will also release unused disk space back to the system. You're out of luck if your storage engine is the older MMAPv1 though; it will still rewrite the collection, but it will not release the unused disk space. Running the compact command places a block on all other operations at the database level, so you have to plan for some downtime.

db.runCommand({compact:'collectionName'})

So let's check it in action with WiredTiger:

> db.files.chunks.storageSize()
394018263040
> db.runCommand({compact:'files.chunks'})
{ "ok" : 1 }
> db.files.chunks.storageSize()
162991509504
>

WoW, we saved more than half of the space :)

If you have a JSON file “js” which you would like to execute on the mongo, you can do as follows:

[root@tbp-mts-mdb02 ~]# /usr/bin/mongo -u root -p "password" --authenticationDatabase=admin --host localhost < script.js
MongoDB shell version v4.2.2
connecting to: mongodb://localhost:27017/?authSource=admin&compressors=disabled&gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("dc5d5def-a7f9-4237-9988-934944d4dedf") }
MongoDB server version: 4.2.2
switched to db incident
{ "nIndexesWas" : 2, "ok" : 1 }
{ "nIndexesWas" : 8, "ok" : 1 }
{ "nIndexesWas" : 7, "ok" : 1 }