Mongod.db will not start--as if /etc/mongod.conf ignored

Carl Seiler

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Feb 15, 2019, 12:35:49 PM2/15/19

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Using MongoDB v4.0.6 installed in Lubuntu 18.0.4.2

/etc/mongod.conf reads as such:

# mongod.conf

# for documentation of all options, see:
#   http://docs.mongodb.org/manual/reference/configuration-options/

# Where and how to store data.
storage:
  dbPath: /media/carl/data/data/db
  journal:
    enabled: true
#  engine:
#  mmapv1:
#  wiredTiger:

# where to write logging data.
systemLog:
  destination: file
  logAppend: true
  path: /media/carl/data/data/db/log/mongod.log

# network interfaces
net:
  port: 27017
  bindIp: 172.17.2.92


# how the process runs
processManagement:
  timeZoneInfo: /usr/share/zoneinfo

#security:

#operationProfiling:

#replication:

#sharding:

## Enterprise-Only Options:

#auditLog:

#snmp:

Ran sudo chown -R mongodb:mongodb /media/carl/data/data/db and sudo chown -R mongodb:mongodb /media/carl/data/data/db/log

because it is my understanding that the service runs as user mongodb per the docs found at https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/

When I attempt to start the service with sudo service mongod start the service fails to start. Typing sudo servuce mongod status gives:

mongod.service - MongoDB Database Server

Loaded: loaded (/lib/systemd/system/mongod.service; disabled; vendor preset:

Active: failed (Result: exit-code) since Fri 2019-02-15 10:40:16 CST; 6s ago

Docs: https://docs.mongodb.org/manual

Process: 3257 ExecStart=/usr/bin/mongod --config /etc/mongod.conf (code=exited

Main PID: 3257 (code=exited, status=1/FAILURE)

Feb 15 10:40:16 carl-VirtualBox systemd[1]: Started MongoDB Database Server.

Feb 15 10:40:16 carl-VirtualBox mongod[3257]: 2019-02-15T10:40:16.154-0600 F CON

Feb 15 10:40:16 carl-VirtualBox systemd[1]: mongod.service: Main process exited,

Feb 15 10:40:16 carl-VirtualBox systemd[1]: mongod.service: Failed with result '

Starting mongod directly from the command line gives:

2019-02-15T11:00:15.374-0600 I CONTROL [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'

2019-02-15T11:00:15.376-0600 I CONTROL [initandlisten] MongoDB starting : pid=3943 port=27017 dbpath=/data/db 64-bit host=carl-VirtualBox

2019-02-15T11:00:15.376-0600 I CONTROL [initandlisten] db version v4.0.6

2019-02-15T11:00:15.376-0600 I CONTROL [initandlisten] git version: caa42a1f75a56c7643d0b68d3880444375ec42e3

2019-02-15T11:00:15.376-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.0g 2 Nov 2017

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] allocator: tcmalloc

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] modules: none

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] build environment:

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] distmod: ubuntu1804

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] distarch: x86_64

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] target_arch: x86_64

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] options: {}

2019-02-15T11:00:15.377-0600 I STORAGE [initandlisten] exception in initAndListen: NonExistentPath: Data directory /data/db not found., terminating

2019-02-15T11:00:15.377-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...

2019-02-15T11:00:15.377-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-27017.sock

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] now exiting

2019-02-15T11:00:15.377-0600 I CONTROL [initandlisten] shutting down with code:100

Note the dbpath=/data/db and Data directory /data/db not found which is where I had it originally before I decided to move it to an xfs file system drive. Mounted at /media/carl/data

It is almost as if it is reading a different /etc/mongod.conf and ignoring the fact that it should now be looking in /media/carl/data/data/db instead. Is there some mongod.conf it is reading, and is there some way I can get it to tell me what mongod.conf that might be?

Thanks

Carl Seiler

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Feb 19, 2019, 11:54:24 AM2/19/19

to mongodb-user

Just for further information, I found that I can start it from the command line using sudo mongod --conf /etc/mongod.conf I still cannot start it with sudo service mongod start

Does the data directory or log directory have to have some certain permission I'm missing? What about /etc/mongod.conf?

File: /media/carl/data/data/db

Size: 4096 Blocks: 8 IO Block: 4096 directory

Device: 811h/2065d Inode: 4194400 Links: 5

Access: (0775/drwxrwxr-x) Uid: ( 112/ mongodb) Gid: ( 123/ mongodb)

Access: 2019-02-19 10:23:37.361184708 -0600

Modify: 2019-02-19 10:46:14.309896087 -0600

Change: 2019-02-19 10:46:14.309896087 -0600

Birth: -

File: /etc/mongod.conf

Size: 648 Blocks: 8 IO Block: 4096 regular file

Device: 801h/2049d Inode: 132118 Links: 1

Access: (0644/-rw-r--r--) Uid: ( 0/ root) Gid: ( 0/ root)

Access: 2019-02-19 09:51:43.690802349 -0600

Modify: 2019-02-15 10:16:29.040495776 -0600

Change: 2019-02-15 10:16:29.040495776 -0600

Birth:

Carl Seiler

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Feb 19, 2019, 4:15:55 PM2/19/19

to mongodb-user

Found that I was missing the init.d file found here:

https://github.com/mongodb/mongo/blob/master/debian/init.d

Now it is clearly reading my mongod.conf file because it is reporting:

Feb 19 14:52:44 carl-VirtualBox mongod[4728]: 2019-02-19T14:52:44.250-0600 F CONTROL [main] Failed global initialization: FileNotOpen: Failed probe for "/media/carl/data/data/db/log/mongod.log": Permission denied

and stat mongod.log yields:

File: mongod.log

Size: 22327 Blocks: 48 IO Block: 4096 regular file

Device: 811h/2065d Inode: 8409185 Links: 1

Access: (0775/-rwxrwxr-x) Uid: ( 112/ mongodb) Gid: ( 123/ mongodb)

Access: 2019-02-19 14:40:21.187815147 -0600

Modify: 2019-02-19 14:36:32.629593148 -0600

Change: 2019-02-19 14:36:32.629593148 -0600

Birth: -

And mongodb appears to be the user specified in the init.d file:

DAEMONUSER=${DAEMONUSER:-mongodb}

DAEMONGROUP=${DAEMONGROUP:-mongodb}

If I'm reading that right. What am I missing?

Oleg Toropov

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Feb 19, 2019, 7:23:38 PM2/19/19

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Did you check permission on folders and file "/media/carl/data/data/db/log/mongod.log"?

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Kevin Adistambha

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Feb 19, 2019, 11:16:54 PM2/19/19

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Hi Carl,

As Oleg mentioned, this sounds like a permission issue in your custom data directory.

The log output from sudo service mongod start you provided appear truncated, but I assume it look similar to this:

● mongod.service - MongoDB Database Server
   Loaded: loaded (/lib/systemd/system/mongod.service; disabled; vendor preset: enabled)
   Active: failed (Result: exit-code) since Wed 2019-02-20 04:05:14 UTC; 3s ago
     Docs: https://docs.mongodb.org/manual
  Process: 2579 ExecStart=/usr/bin/mongod --config /etc/mongod.conf (code=exited, status=1/FAILURE)
 Main PID: 2579 (code=exited, status=1/FAILURE)

Feb 20 04:05:14 xxxx systemd[1]: Started MongoDB Database Server.
Feb 20 04:05:14 xxxx mongod[2579]: 2019-02-20T04:05:14.761+0000 F CONTROL  [main] Failed global initialization: FileNotOpen: Failed to open "/media/mdb/data/mongod.log"
Feb 20 04:05:14 xxxx systemd[1]: mongod.service: Main process exited, code=exited, status=1/FAILURE
Feb 20 04:05:14 xxxx systemd[1]: mongod.service: Failed with result 'exit-code'.

Note the line Failed to open ... above. Is your output showing similar thing? In my experiment, this was caused by the mongodb user not having access to the directory /media/mdb/data.

You might want to double check if the directories /media, /media/carl, /media/carl/data are all world-executable (permission set to at least 755).

Best regards,
Kevin

Carl Seiler

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Feb 20, 2019, 9:38:01 AM2/20/19

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Thank you Oleg and Kevin,

I know we are on the right track here, and I have been setting the permissions on everything. Just to make sure I went through and did:

sudo chmod 755 /media

sudo chmod 755 /media/carl

sudo chmod 755 /media/carl/data

sudo chmod 755 /media/carl/data/data

When I go through, each of them have permissions 755 now. /media/carl/data/data has 775 and belongs to mongodb:mongodb, and the same with /media/carl/data/data/db/log

So I attempt to start the service:

sudo service mongod start

When I do sudo service mongo status I get (sorry about the truncated version in earlier post):

● mongod.service - MongoDB Database Server

Loaded: loaded (/lib/systemd/system/mongod.service; enabled; vendor preset: enabled)

Active: failed (Result: exit-code) since Wed 2019-02-20 08:12:27 CST; 2s ago

Docs: https://docs.mongodb.org/manual

Process: 2639 ExecStart=/usr/bin/mongod --config /etc/mongod.conf (code=exited, status=14)

Main PID: 2639 (code=exited, status=14)

Feb 20 08:12:26 carl-VirtualBox systemd[1]: Started MongoDB Database Server.

Feb 20 08:12:27 carl-VirtualBox systemd[1]: mongod.service: Main process exited, code=exited, status=14/n/a

Feb 20 08:12:27 carl-VirtualBox systemd[1]: mongod.service: Failed with result 'exit-code'.

Note that I'm not getting the "failed to open" although I was getting that a few days ago when I first posted the problem.

However, I am clearly now getting better logging now that my service process can write to the log file:

2019-02-20T08:12:27.225-0600 E STORAGE [initandlisten] WiredTiger error (13) [1550671947:225035][2639:0x7f80a0945a40], connection: __directory_list_worker, 48: /media/carl/data/data/db/journal: directory-list: opendir: Permission denied Raw: [1550671947:225035][2639:0x7f80a0945a40], connection: __directory_list_worker, 48: /media/carl/data/data/db/journal: directory-list: opendir: Permission denied

2019-02-20T08:12:27.230-0600 E STORAGE [initandlisten] WiredTiger error (13) [1550671947:230011][2639:0x7f80a0945a40], connection: __directory_list_worker, 48: /media/carl/data/data/db/journal: directory-list: opendir: Permission denied Raw: [1550671947:230011][2639:0x7f80a0945a40], connection: __directory_list_worker, 48: /media/carl/data/data/db/journal: directory-list: opendir: Permission denied

2019-02-20T08:12:27.231-0600 W STORAGE [initandlisten] Failed to start up WiredTiger under any compatibility version.

2019-02-20T08:12:27.231-0600 F STORAGE [initandlisten] Reason: 13: Permission denied

2019-02-20T08:12:27.231-0600 F - [initandlisten] Fatal Assertion 28595 at src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 704

2019-02-20T08:12:27.231-0600 F - [initandlisten]

***aborting after fassert() failure

So, I changed ownership on the directory /media/carl/data/data/db/journal to mongodb and changed permissions to 755 and TADA!

I think it was permissions on the journal directory and my logging directory. The journal directory was causing the main problem and I couldn't at first see what the problem was because it wasn't able to write to the log. The journal directory belonged to my main user and not mongodb. I think it was created when I ran it from simply running mongod --config /etc/mongod.conf Thereafter, running as a service couldn't get it to work because it belonged to user carl not mongodb.

Thanks for pointing me in the right direction. I just had to keep digging for the permissions for the right directory.

Oleg Toropov

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Feb 20, 2019, 3:39:54 PM2/20/19

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Glad it works out for you... I have a script somewhere that goes and change permission/owner for all tree sub-directories...

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