Fresh install mongodb on Ubuntu - After running mongo command mongod disappears

Nathan Nass

unread,

Jun 12, 2014, 11:33:08 AM6/12/14

to mongod...@googlegroups.com

Hello,

I am new to mongodb and was trying to install on ubuntu 14.04 via the instructions in the mongo manual. I originally was able to run mongodb, but after a time the installation did not work. I tried to to a fresh install of mongodb, and again it worked for a brief time but then failed. I investigated the /usr/bin folder, but it seems that mongod has disappeared. I am wondering if I missed some configuration or installation step?

For reference I have included the complete terminal output and partial log file for the final installation attempt.

Thank you,

Nathan

usr1@httpQuery:~/httpProject/httptest$ sudo apt-get install mongodb-org

Reading package lists... Done

Building dependency tree

Reading state information... Done

The following extra packages will be installed:

mongodb-org-mongos mongodb-org-server mongodb-org-shell mongodb-org-tools

The following NEW packages will be installed:

mongodb-org mongodb-org-mongos mongodb-org-server mongodb-org-shell mongodb-org-tools

0 upgraded, 5 newly installed, 0 to remove and 69 not upgraded.

Need to get 0 B/114 MB of archives.

After this operation, 287 MB of additional disk space will be used.

Do you want to continue? [Y/n] Y

Selecting previously unselected package mongodb-org-shell.

(Reading database ... 62259 files and directories currently installed.)

Preparing to unpack .../mongodb-org-shell_2.6.1_amd64.deb ...

Unpacking mongodb-org-shell (2.6.1) ...

Selecting previously unselected package mongodb-org-server.

Preparing to unpack .../mongodb-org-server_2.6.1_amd64.deb ...

Unpacking mongodb-org-server (2.6.1) ...

Selecting previously unselected package mongodb-org-mongos.

Preparing to unpack .../mongodb-org-mongos_2.6.1_amd64.deb ...

Unpacking mongodb-org-mongos (2.6.1) ...

Selecting previously unselected package mongodb-org-tools.

Preparing to unpack .../mongodb-org-tools_2.6.1_amd64.deb ...

Unpacking mongodb-org-tools (2.6.1) ...

Selecting previously unselected package mongodb-org.

Preparing to unpack .../mongodb-org_2.6.1_amd64.deb ...

Unpacking mongodb-org (2.6.1) ...

Processing triggers for man-db (2.6.7.1-1) ...

Processing triggers for ureadahead (0.100.0-16) ...

Setting up mongodb-org-shell (2.6.1) ...

Setting up mongodb-org-server (2.6.1) ...

mongod start/running, process 29466

Setting up mongodb-org-mongos (2.6.1) ...

Setting up mongodb-org-tools (2.6.1) ...

Setting up mongodb-org (2.6.1) ...

usr1@httpQuery:~/httpProject/httptest$ which mongod

/usr/bin/mongod

usr1@httpQuery:~/httpProject/httptest$ mongod -version

db version v2.6.1

2014-06-12T10:56:04.440-0400 git version: 4b95b086d2374bdcfcdf2249272fb552c9c726e8

usr1@httpQuery:~/httpProject/httptest$ sudo service mongod status

mongod start/running, process 29466

usr1@httpQuery:~/httpProject/httptest$ sudo service mongod stop

mongod stop/waiting

usr1@httpQuery:~/httpProject/httptest$ sudo service mongod start

mongod start/running, process 29537

usr1@httpQuery:~/httpProject/httptest$ sudo service mongod restart

mongod stop/waiting

mongod start/running, process 29570

usr1@httpQuery:~/httpProject/httptest$ mongo

MongoDB shell version: 2.6.1

connecting to: test

> quit()

usr1@httpQuery:~/httpProject/httptest$ sudo service mongod status

mongod start/running, process 29570

usr1@httpQuery:~/httpProject/httptest$ which mongo

/usr/bin/mongo

usr1@httpQuery:~/httpProject/httptest$ which mongod

/usr/bin/mongod

usr1@httpQuery:~/httpProject/httptest$ which mongodb

usr1@httpQuery:~/httpProject/httptest$ mongo

MongoDB shell version: 2.6.1

connecting to: test

2014-06-12T11:10:16.901-0400 warning: Failed to connect to 127.0.0.1:27017, reason: errno:111 Connection refused

2014-06-12T11:10:16.902-0400 Error: couldn't connect to server 127.0.0.1:27017 (127.0.0.1), connection attempt failed at src/mongo/shell/mongo.js:146

exception: connect failed

usr1@httpQuery:~/httpProject/httptest$ which mongod

usr1@httpQuery:~/httpProject/httptest$

..... Log output

2014-06-12T10:54:59.702-0400 [FileAllocator] done allocating datafile /var/lib/mongodb/local.0, size: 64MB, took 0.001 secs

2014-06-12T10:54:59.704-0400 [initandlisten] build index on: local.startup_log properties: { v: 1, key: { _id: 1 }, name: "_id_", ns: "local.startup_log" }

2014-06-12T10:54:59.705-0400 [initandlisten] added index to empty collection

2014-06-12T10:54:59.705-0400 [initandlisten] waiting for connections on port 27017

2014-06-12T10:55:59.693-0400 [clientcursormon] mem (MB) res:35 virt:349

2014-06-12T10:55:59.693-0400 [clientcursormon] mapped (incl journal view):160

2014-06-12T10:55:59.693-0400 [clientcursormon] connections:0

2014-06-12T10:56:33.269-0400 [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends

2014-06-12T10:56:33.269-0400 [signalProcessingThread] now exiting

2014-06-12T10:56:33.269-0400 [signalProcessingThread] dbexit:

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: going to close listening sockets...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] closing listening socket: 8

2014-06-12T10:56:33.269-0400 [signalProcessingThread] closing listening socket: 9

2014-06-12T10:56:33.269-0400 [signalProcessingThread] removing socket file: /tmp/mongodb-27017.sock

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: going to flush diaglog...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: going to close sockets...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: waiting for fs preallocator...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: lock for final commit...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: final commit...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] shutdown: closing all files...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] closeAllFiles() finished

2014-06-12T10:56:33.269-0400 [signalProcessingThread] journalCleanup...

2014-06-12T10:56:33.269-0400 [signalProcessingThread] removeJournalFiles

2014-06-12T10:56:33.272-0400 [signalProcessingThread] shutdown: removing fs lock...

2014-06-12T10:56:33.272-0400 [signalProcessingThread] dbexit: really exiting now

2014-06-12T10:56:36.642-0400 ***** SERVER RESTARTED *****

2014-06-12T10:56:36.648-0400 [initandlisten] MongoDB starting : pid=29537 port=27017 dbpath=/var/lib/mongodb 64-bit host=httpQuery

2014-06-12T10:56:36.648-0400 [initandlisten] db version v2.6.1

2014-06-12T10:56:36.648-0400 [initandlisten] git version: 4b95b086d2374bdcfcdf2249272fb552c9c726e8

2014-06-12T10:56:36.648-0400 [initandlisten] build info: Linux build14.nj1.10gen.cc 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 BOOST_LIB_VERSION=1_49

2014-06-12T10:56:36.648-0400 [initandlisten] allocator: tcmalloc

2014-06-12T10:56:36.648-0400 [initandlisten] options: { config: "/etc/mongod.conf", net: { bindIp: "127.0.0.1" }, storage: { dbPath: "/var/lib/mongodb" }, systemLog: { destination: "file", logAppend: true, path: "/var/log/mongodb/mongod.log" } }

2014-06-12T10:56:36.650-0400 [initandlisten] journal dir=/var/lib/mongodb/journal

2014-06-12T10:56:36.650-0400 [initandlisten] recover : no journal files present, no recovery needed

2014-06-12T10:56:36.740-0400 [initandlisten] waiting for connections on port 27017

2014-06-12T10:56:40.900-0400 [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends

2014-06-12T10:56:40.900-0400 [signalProcessingThread] now exiting

2014-06-12T10:56:40.900-0400 [signalProcessingThread] dbexit:

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: going to close listening sockets...

2014-06-12T10:56:40.900-0400 [signalProcessingThread] closing listening socket: 8

2014-06-12T10:56:40.900-0400 [signalProcessingThread] closing listening socket: 9

2014-06-12T10:56:40.900-0400 [signalProcessingThread] removing socket file: /tmp/mongodb-27017.sock

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: going to flush diaglog...

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: going to close sockets...

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: waiting for fs preallocator...

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: lock for final commit...

2014-06-12T10:56:40.900-0400 [signalProcessingThread] shutdown: final commit...

2014-06-12T10:56:40.906-0400 [signalProcessingThread] shutdown: closing all files...

2014-06-12T10:56:40.906-0400 [signalProcessingThread] closeAllFiles() finished

2014-06-12T10:56:40.906-0400 [signalProcessingThread] journalCleanup...

2014-06-12T10:56:40.906-0400 [signalProcessingThread] removeJournalFiles

2014-06-12T10:56:40.908-0400 [signalProcessingThread] shutdown: removing fs lock...

2014-06-12T10:56:40.908-0400 [signalProcessingThread] dbexit: really exiting now

2014-06-12T10:56:41.038-0400 ***** SERVER RESTARTED *****

2014-06-12T10:56:41.046-0400 [initandlisten] MongoDB starting : pid=29570 port=27017 dbpath=/var/lib/mongodb 64-bit host=httpQuery

2014-06-12T10:56:41.046-0400 [initandlisten] db version v2.6.1

2014-06-12T10:56:41.046-0400 [initandlisten] git version: 4b95b086d2374bdcfcdf2249272fb552c9c726e8

2014-06-12T10:56:41.046-0400 [initandlisten] build info: Linux build14.nj1.10gen.cc 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 BOOST_LIB_VERSION=1_49

2014-06-12T10:56:41.046-0400 [initandlisten] allocator: tcmalloc

2014-06-12T10:56:41.046-0400 [initandlisten] options: { config: "/etc/mongod.conf", net: { bindIp: "127.0.0.1" }, storage: { dbPath: "/var/lib/mongodb" }, systemLog: { destination: "file", logAppend: true, path: "/var/log/mongodb/mongod.log" } }

2014-06-12T10:56:41.051-0400 [initandlisten] journal dir=/var/lib/mongodb/journal

2014-06-12T10:56:41.051-0400 [initandlisten] recover : no journal files present, no recovery needed

2014-06-12T10:56:41.172-0400 [initandlisten] waiting for connections on port 27017

2014-06-12T10:56:44.654-0400 [initandlisten] connection accepted from 127.0.0.1:37045 #1 (1 connection now open)

2014-06-12T10:56:54.461-0400 [conn1] end connection 127.0.0.1:37045 (0 connections now open)

2014-06-12T10:57:41.167-0400 [clientcursormon] mem (MB) res:35 virt:350

2014-06-12T10:57:41.167-0400 [clientcursormon] mapped (incl journal view):160

2014-06-12T10:57:41.167-0400 [clientcursormon] connections:0

usr1@httpQuery:~/httpProject/httptest$

Ernie Hershey

unread,

Jun 12, 2014, 11:48:22 AM6/12/14

to mongodb-user

Hi Nathan,

That's really strange. Is it possible another process on the same machine uninstalled the mongodb-org-server package?

If you run this does it show all the mongodb-org packages?

dpkg-query -l 'mongodb-org*'

Ernie

--
You received this message because you are subscribed to the Google Groups "mongodb-user"
group.

For other MongoDB technical support options, see: http://www.mongodb.org/about/support/.
---
You received this message because you are subscribed to the Google Groups "mongodb-user" group.
To unsubscribe from this group and stop receiving emails from it, send an email to mongodb-user...@googlegroups.com.
To post to this group, send email to mongod...@googlegroups.com.
Visit this group at http://groups.google.com/group/mongodb-user.
To view this discussion on the web visit https://groups.google.com/d/msgid/mongodb-user/766f0126-1aea-41c7-ade9-29254cebbae6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Nathan Nass

unread,

Jun 12, 2014, 12:12:21 PM6/12/14

to mongod...@googlegroups.com

Hi Ernie,

I am not sure if another process would have uninstalled it. I am running a recently allocated vm on a shared hosting service, so I don't think so. I had originally tried working with the clojure driver monger, and I was able to insert one record following the tutorial before the original install stopped working. Since I tried a fresh install and the same result happened without using the clojure driver (ie just using the command line as indicated above) I am not sure whether it is related.

When I run dpkg, I just get the mongodb-org packages along with the unstable versions

usr1@httpQuery:~/httpProject/httptest$ dpkg-query -l 'mongodb-org*'

Desired=Unknown/Install/Remove/Purge/Hold

| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend

|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)

||/ Name Version Architecture Description

+++-=====================-===============-===============-===============================================

ii mongodb-org 2.6.1 amd64 MongoDB open source document-oriented database

ii mongodb-org-mongos 2.6.1 amd64 MongoDB sharded cluster query router

ii mongodb-org-server 2.6.1 amd64 MongoDB database server

ii mongodb-org-shell 2.6.1 amd64 MongoDB shell client

ii mongodb-org-tools 2.6.1 amd64 MongoDB tools

un mongodb-org-unstable <none> <none> (no description available)

un mongodb-org-unstable- <none> <none> (no description available)

These are the files that remain in the /usr/bin directory:

usr1@httpQuery:~/httpProject/httptest$ ls -l /usr/bin/ | grep mongo

-rwxr-xr-x 1 root root 11871000 May 5 11:13 mongo

-rwxr-xr-x 1 root root 23408296 May 5 11:13 mongodump

-rwxr-xr-x 1 root root 23352616 May 5 11:13 mongoexport

-rwxr-xr-x 1 root root 23400504 May 5 11:13 mongofiles

-rwxr-xr-x 1 root root 23375272 May 5 11:13 mongoimport

-rwxr-xr-x 1 root root 23345384 May 5 11:13 mongooplog

-rwxr-xr-x 1 root root 23156920 May 5 11:13 mongoperf

-rwxr-xr-x 1 root root 23443528 May 5 11:13 mongorestore

-rwxr-xr-x 1 root root 18252920 May 5 11:13 mongos

-rwxr-xr-x 1 root root 23397576 May 5 11:13 mongostat

-rwxr-xr-x 1 root root 23340712 May 5 11:13 mongotop

Thank you,

Nathan

Victor Hooi

unread,

Jun 16, 2014, 1:47:02 AM6/16/14

to mongod...@googlegroups.com

Hi Nathan,

Your dpkg-query output is showing that the MongoDB 2.6.1 packages are actually still installed. However, your /usr/bin/mongod binary itself is missing. As Ernie said, this is rather strange. Before you re-install anything, can you please run the following and reply here with the output:

sudo grep -B 3 -i mongo /var/log/apt/history.log
sudo zgrep -B 3 -i mongo /var/log/apt/history.log.*.gz

This will give us the installation/uninstallation events around MongoDB.

You can then reinstall the mongodb-org-server package with the following command:

sudo apt-get install --reinstall mongodb-org-serve

Please let me know if you have any queries about any of the above.

Regards,

Victor

Nathan Nass

unread,

Jun 16, 2014, 9:28:07 AM6/16/14

to mongod...@googlegroups.com

Hi Victor,

Thank you for your reply. I received a note from support today about the server that was running that instance of mongo. It appears that it was compromised, and they disabled ssh access to it, so I don't think I can investigate it further. But I would assume that this strange behavior is related to this compromise. I am not sure why only mongod would be removed leaving the other files. This weekend, I was able to create a new server with an instance of mondo db using the same setup, and it appears to be functioning well. If I get a chance to access the server again I will try to read those log files and post the information here.