MongoDB won't start as a service?

Question

I'm having some trouble debugging why my MongoDB won't start as a service. Starting it normally (just running "mongod") seems to work fine. But when I run it as a service, the below log results. I have tried removing fslock and changing ownership of a couple directories on various posts from Googling, but I am stuck.

The ownership of /data/db is as follows:

root@debian:/home/sjohnson# ls -ld /data/db
drwxr-xr-x 4 mongodb mongodb 4096 Sep 26 17:18 /data/db

Likewise, here is /var/lib/mongod:

root@debian:/home/sjohnson# ls -ld /var/lib/mongodb
drwxr-xr-x 3 mongodb mongodb 4096 Sep 26 16:54 /var/lib/mongodb

Here is the log file:

root@debian:/home/sjohnson# sudo -u mongodb mongod --dbpath /var/lib/mongodb/
Sat Sep 26 17:27:11 [initandlisten] MongoDB starting : pid=5615 port=27017 dbpath=/var/lib/mongodb/ 64-bit host=debian
Sat Sep 26 17:27:11 [initandlisten] db version v2.0.6, pdfile version 4.5
Sat Sep 26 17:27:11 [initandlisten] git version: nogitversion
Sat Sep 26 17:27:11 [initandlisten] build info: Linux z6 3.8-trunk-amd64 #1 SMP Debian 3.8.3-1~experimental.1 x86_64 BOOST_LIB_VERSION=1_49
Sat Sep 26 17:27:11 [initandlisten] options: { dbpath: "/var/lib/mongodb/" }
Sat Sep 26 17:27:11 [initandlisten] journal dir=/var/lib/mongodb/journal
Sat Sep 26 17:27:11 [initandlisten] recover : no journal files present, no recovery needed
Sat Sep 26 17:27:11 [initandlisten] ****
Sat Sep 26 17:27:11 [initandlisten] ****
Sat Sep 26 17:27:11 [initandlisten] need to upgrade database SteveIsAwesome with pdfile version 4.22, new version: 4.5
Sat Sep 26 17:27:11 [initandlisten]      Not upgrading, exiting
Sat Sep 26 17:27:11 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:27:11 [initandlisten] ****
Sat Sep 26 17:27:11 dbexit: 
Sat Sep 26 17:27:11 [initandlisten] shutdown: going to close listening sockets...
Sat Sep 26 17:27:11 [initandlisten] shutdown: going to flush diaglog...
Sat Sep 26 17:27:11 [initandlisten] shutdown: going to close sockets...
Sat Sep 26 17:27:11 [initandlisten] shutdown: waiting for fs preallocator...
Sat Sep 26 17:27:11 [initandlisten] shutdown: lock for final commit...
Sat Sep 26 17:27:11 [initandlisten] shutdown: final commit...
Sat Sep 26 17:27:11 [initandlisten] shutdown: closing all files...
Sat Sep 26 17:27:11 [initandlisten] closeAllFiles() finished
Sat Sep 26 17:27:11 [initandlisten] journalCleanup...
Sat Sep 26 17:27:11 [initandlisten] removeJournalFiles
Sat Sep 26 17:27:11 [initandlisten] shutdown: removing fs lock...
Sat Sep 26 17:27:11 dbexit: really exiting now
Logstream::get called in uninitialized state
Sat Sep 26 17:27:11 [initandlisten] ERROR: Client::~Client _context should be null but is not; client:initandlisten
root@debian:/home/sjohnson# tail -f -n50 /var/log/mongodb/mongodb.log
Sat Sep 26 17:25:00 [initandlisten] MongoDB starting : pid=5318 port=27017 dbpath=/var/lib/mongodb 64-bit host=debian
Sat Sep 26 17:25:00 [initandlisten] db version v2.0.6, pdfile version 4.5
Sat Sep 26 17:25:00 [initandlisten] git version: nogitversion
Sat Sep 26 17:25:00 [initandlisten] build info: Linux z6 3.8-trunk-amd64 #1 SMP Debian 3.8.3-1~experimental.1 x86_64 BOOST_LIB_VERSION=1_49
Sat Sep 26 17:25:00 [initandlisten] options: { bind_ip: "127.0.0.1", command: [ "run" ], config: "/etc/mongodb.conf", dbpath: "/var/lib/mongodb", journal: "true", logappend: "true", logpath: "/var/log/mongodb/mongodb.log", unixSocketPrefix: "/var/run/mongodb" }
Sat Sep 26 17:25:00 [initandlisten] journal dir=/var/lib/mongodb/journal
Sat Sep 26 17:25:00 [initandlisten] recover : no journal files present, no recovery needed
Sat Sep 26 17:25:00 [initandlisten] ****
Sat Sep 26 17:25:00 [initandlisten] ****
Sat Sep 26 17:25:00 [initandlisten] need to upgrade database SteveIsAwesome with pdfile version 4.22, new version: 4.5
Sat Sep 26 17:25:00 [initandlisten]      Not upgrading, exiting
Sat Sep 26 17:25:00 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:25:00 [initandlisten] ****
Sat Sep 26 17:25:00 dbexit: 
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to close listening sockets...
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to flush diaglog...
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to close sockets...
Sat Sep 26 17:25:00 [initandlisten] shutdown: waiting for fs preallocator...
Sat Sep 26 17:25:00 [initandlisten] shutdown: lock for final commit...
Sat Sep 26 17:25:00 [initandlisten] shutdown: final commit...
Sat Sep 26 17:25:00 [initandlisten] shutdown: closing all files...
Sat Sep 26 17:25:00 [initandlisten] closeAllFiles() finished
Sat Sep 26 17:25:00 [initandlisten] journalCleanup...
Sat Sep 26 17:25:00 [initandlisten] removeJournalFiles
Sat Sep 26 17:25:00 [initandlisten] shutdown: removing fs lock...
Sat Sep 26 17:25:00 dbexit: really exiting now
Logstream::get called in uninitialized state
Sat Sep 26 17:25:00 [initandlisten] ERROR: Client::~Client _context should be null but is not; client:initandlisten

Edit:

Update: upgraded database per comment with mongod --upgrade. Showed no errors per:

root@debian:/var/lib/mongodb# tail -f -n50 /var/log/mongodb/mongodb.log
Sat Sep 26 17:25:00 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:25:00 [initandlisten] ****
Sat Sep 26 17:25:00 dbexit: 
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to close listening sockets...
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to flush diaglog...
Sat Sep 26 17:25:00 [initandlisten] shutdown: going to close sockets...
Sat Sep 26 17:25:00 [initandlisten] shutdown: waiting for fs preallocator...
Sat Sep 26 17:25:00 [initandlisten] shutdown: lock for final commit...
Sat Sep 26 17:25:00 [initandlisten] shutdown: final commit...
Sat Sep 26 17:25:00 [initandlisten] shutdown: closing all files...
Sat Sep 26 17:25:00 [initandlisten] closeAllFiles() finished
Sat Sep 26 17:25:00 [initandlisten] journalCleanup...
Sat Sep 26 17:25:00 [initandlisten] removeJournalFiles
Sat Sep 26 17:25:00 [initandlisten] shutdown: removing fs lock...
Sat Sep 26 17:25:00 dbexit: really exiting now
Logstream::get called in uninitialized state
Sat Sep 26 17:25:00 [initandlisten] ERROR: Client::~Client _context should be null but is not; client:initandlisten

But service still fails to start. Tailing show:

root@debian:/var/lib/mongodb# tail -f -n50 /var/log/mongodb/mongodb.log
Sat Sep 26 17:49:52 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:49:52 [initandlisten] ****
Sat Sep 26 17:49:52 dbexit: 
Sat Sep 26 17:49:52 [initandlisten] shutdown: going to close listening sockets...
Sat Sep 26 17:49:52 [initandlisten] shutdown: going to flush diaglog...
Sat Sep 26 17:49:52 [initandlisten] shutdown: going to close sockets...
Sat Sep 26 17:49:52 [initandlisten] shutdown: waiting for fs preallocator...
Sat Sep 26 17:49:52 [initandlisten] shutdown: lock for final commit...
Sat Sep 26 17:49:52 [initandlisten] shutdown: final commit...
Sat Sep 26 17:49:52 [initandlisten] shutdown: closing all files...
Sat Sep 26 17:49:52 [initandlisten] closeAllFiles() finished
Sat Sep 26 17:49:52 [initandlisten] journalCleanup...
Sat Sep 26 17:49:52 [initandlisten] removeJournalFiles
Sat Sep 26 17:49:52 [initandlisten] shutdown: removing fs lock...
Sat Sep 26 17:49:52 dbexit: really exiting now
Logstream::get called in uninitialized state
Sat Sep 26 17:49:52 [initandlisten] ERROR: Client::~Client _context should be null but is not; client:initandlisten


***** SERVER RESTARTED *****


Sat Sep 26 17:50:30 [initandlisten] MongoDB starting : pid=9104 port=27017 dbpath=/var/lib/mongodb 64-bit host=debian
Sat Sep 26 17:50:30 [initandlisten] db version v2.0.6, pdfile version 4.5
Sat Sep 26 17:50:30 [initandlisten] git version: nogitversion
Sat Sep 26 17:50:30 [initandlisten] build info: Linux z6 3.8-trunk-amd64 #1 SMP Debian 3.8.3-1~experimental.1 x86_64 BOOST_LIB_VERSION=1_49
Sat Sep 26 17:50:30 [initandlisten] options: { bind_ip: "127.0.0.1", command: [ "run" ], config: "/etc/mongodb.conf", dbpath: "/var/lib/mongodb", journal: "true", logappend: "true", logpath: "/var/log/mongodb/mongodb.log", unixSocketPrefix: "/var/run/mongodb" }
Sat Sep 26 17:50:30 [initandlisten] journal dir=/var/lib/mongodb/journal
Sat Sep 26 17:50:30 [initandlisten] recover : no journal files present, no recovery needed
Sat Sep 26 17:50:30 [initandlisten] ****
Sat Sep 26 17:50:30 [initandlisten] ****
Sat Sep 26 17:50:30 [initandlisten] need to upgrade database local with pdfile version 4.22, new version: 4.5
Sat Sep 26 17:50:30 [initandlisten]      Not upgrading, exiting
Sat Sep 26 17:50:30 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:50:30 [initandlisten] ****
Sat Sep 26 17:50:30 dbexit: 
Sat Sep 26 17:50:30 [initandlisten] shutdown: going to close listening sockets...
Sat Sep 26 17:50:30 [initandlisten] shutdown: going to flush diaglog...
Sat Sep 26 17:50:30 [initandlisten] shutdown: going to close sockets...
Sat Sep 26 17:50:30 [initandlisten] shutdown: waiting for fs preallocator...
Sat Sep 26 17:50:30 [initandlisten] shutdown: lock for final commit...
Sat Sep 26 17:50:30 [initandlisten] shutdown: final commit...
Sat Sep 26 17:50:30 [initandlisten] shutdown: closing all files...
Sat Sep 26 17:50:30 [initandlisten] closeAllFiles() finished
Sat Sep 26 17:50:30 [initandlisten] journalCleanup...
Sat Sep 26 17:50:30 [initandlisten] removeJournalFiles
Sat Sep 26 17:50:30 [initandlisten] shutdown: removing fs lock...
Sat Sep 26 17:50:30 dbexit: really exiting now
Logstream::get called in uninitialized state
Sat Sep 26 17:50:30 [initandlisten] ERROR: Client::~Client _context should be null but is not; client:initandlisten

Answer 1

Sat Sep 26 17:27:11 [initandlisten] need to upgrade database SteveIsAwesome with pdfile version 4.22, new version: 4.5
Sat Sep 26 17:27:11 [initandlisten]      Not upgrading, exiting
Sat Sep 26 17:27:11 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:27:11 [initandlisten] ****

Did you try to run it with --upgrade?

UPDATED

Sat Sep 26 17:50:30 [initandlisten] need to upgrade database local with pdfile version 4.22, new version: 4.5
Sat Sep 26 17:50:30 [initandlisten]      Not upgrading, exiting
Sat Sep 26 17:50:30 [initandlisten]      run --upgrade to upgrade dbs, then start again
Sat Sep 26 17:50:30 [initandlisten] ****

Db change? Maybe it's upgrading once db per run.