I am trying to run mongo in a LSF cluster computing environment where I
have no admin control.

Our sysadmin installed mongodb, but it is not running. Any ideas on what
should I ask the server admin to do for it to run? Or if I could run it
locally?

[node1382]allelix> mongod --dbpath /users/dnaiel/ma/mongodb/
Tue Oct  2 21:33:48 [initandlisten] MongoDB starting : pid=22436 port=27017     dbpath=/seq/epigenome01/allelix/ma/mongodb/ 64-bit host=node1382
Tue Oct  2 21:33:48 [initandlisten]
Tue Oct  2 21:33:48 [initandlisten] ** WARNING: You are running on a NUMA machine.
Tue Oct  2 21:33:48 [initandlisten] **          We suggest launching mongod like this to    avoid performance problems:
Tue Oct  2 21:33:48 [initandlisten] **              numactl --interleave=all mongod [other options]
Tue Oct  2 21:33:48 [initandlisten]
Tue Oct  2 21:33:48 [initandlisten] db version v2.2.0, pdfile version 4.5
Tue Oct  2 21:33:48 [initandlisten] git version: f5e83eae9cfbec7fb7a071321928f00d1b0c5207
Tue Oct  2 21:33:48 [initandlisten] build info: Linux ip-10-2-29-40 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64 BOOST_LIB_VERSION=1_49
Tue Oct  2 21:33:48 [initandlisten] options: { dbpath: "/users/dnaiel/ma/mongodb/" }
Tue Oct  2 21:33:48 [initandlisten] journal dir=users/dnaiel/ma/mongodb/journal
Tue Oct  2 21:33:48 [initandlisten] recover begin
Tue Oct  2 21:33:48 [initandlisten] info no lsn file in journal/ directory
Tue Oct  2 21:33:48 [initandlisten] recover lsn: 0
Tue Oct  2 21:33:48 [initandlisten] recover /seq/epigenome01/allelix/ma/mongodb/journal/j._0
Tue Oct  2 21:33:48 [initandlisten] recover cleaning up
Tue Oct  2 21:33:48 [initandlisten] removeJournalFiles
Tue Oct  2 21:33:48 [initandlisten] recover done
Tue Oct  2 21:33:48 [websvr] admin web console waiting for connections on port 28017
Tue Oct  2 21:33:48 [initandlisten] waiting for connections on port 27017

It basically waits forever and cannot start mongodb. These servers are not
webservers but they do have network access, it's a cloud computing LSF
environment system.

Any advice would be welcome, thanks in advance.

Hi Daniel,

Beyond the NUMA warnings everything there looks normal.

Mongod appears to be up and waiting for client connections.

What are you expecting?

Cheers,

David

Hi, I guess I am confused as on how to use mongodb then.  I have used it in
my own amazon ec2 server and have no problem when I type mongo, but ...

in this server I try the following and it would not connect:

Prepending: .mongodb-linux-x86_64-2.2.0 (ok)
allelix> mongo
MongoDB shell version: 2.2.0
connecting to: test
Mon Oct  8 22:47:49 Error: couldn't connect to server 127.0.0.1:27017
 src/mongo/shell/mongo.js:91
exception: connect failed

so i am not sure what to do or what could be the issue.  maybe a firewall
blocking issue?

Are you running the mongo command on the same server that you have mongod
running on? *yes, I do.  As I said I have no server admin permissions so I
have no idea how to solve this issue.*

If you are, then can you check that the process is running while you try
and connect?  *How'd I do this?*

If the process is running then yes, there could be a firewall blocking
loopback connections on that port.  *How could I solve this?*

Daniel,

To check for a running mongod process, please try the following command "ps
-ef | grep mongod"

To check simple connectivity you should try the telnet command.

The syntax to check would be, "telnet 127.0.0.1 27017" this will try and
connect to the mongod port.

To exit telnet press Ctrl + ] which will give you a prompt then type quit.

Cheers,

David

Hi David, thanks a lot.

I tried the commands you suggested and these are the results:

allelix> ps -ef | grep mongod
dfernand 30839 22317  0 13:41 pts/132  00:00:00 grep mongod

allelix> telnet 127.0.0.1 27017
Trying 127.0.0.1...
telnet: connect to address 127.0.0.1: Connection refused
telnet: Unable to connect to remote host: Connection refused

[tin.broadinstitute.org]allelix> mongod --dbpath
/seq/epigenome01/allelix/ma/mongodb/
Wed Oct 10 13:42:15 [initandlisten] MongoDB starting : pid=32011 port=27017
dbpath=/seq/epigenome01/allelix/ma/mongodb/ 64-bit
host=tin.broadinstitute.org
Wed Oct 10 13:42:15 [initandlisten] db version v2.2.0, pdfile version 4.5
Wed Oct 10 13:42:15 [initandlisten] git version:
f5e83eae9cfbec7fb7a071321928f00d1b0c5207
Wed Oct 10 13:42:15 [initandlisten] build info: Linux ip-10-2-29-40
2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64
BOOST_LIB_VERSION=1_49
Wed Oct 10 13:42:15 [initandlisten] options: { dbpath:
"/seq/epigenome01/allelix/ma/mongodb/" }
Wed Oct 10 13:42:15 [initandlisten] journal
dir=/seq/epigenome01/allelix/ma/mongodb/journal
Wed Oct 10 13:42:15 [initandlisten] recover : no journal files present, no
recovery needed
Wed Oct 10 13:42:15 [initandlisten] waiting for connections on port 27017
Wed Oct 10 13:42:15 [websvr] admin web console waiting for connections on
port 28017

So my question would be how can I set it up, I do not have admin permission
over these servers so I am not sure how to proceed.  Do you have any
suggestion as what the admin team would have to do to allow the
usage/connection to the server for mongodb.

ThANKS!

Right, the first two commands showed that your mongod instance was not
running when you tried to connect to it.

My suggestion for you now is to do the following:

Add options to set the logpath of your mongod instance and the fork. These
are --logpath <path to file> and --fork

This means mongo will run in the background. You can see details on the
mongod commands here
http://docs.mongodb.org/manual/reference/mongod/

MongoDB is run in a number of parts, mongod is the actual DB server that
stores your data.
The "mongo" application is the MongoDB shell client, which gives you an
interface into the server.
By the looks of things you did not have your server running when you tried
to connect to it with your client.
Adding the fork and logpath options will allow mongod to run in the
background so it can run without intervention.

Once its up and running in the background you can use "ps -ef | grep
mongod" to check if the process is running and then connect with the mongo
shell application.

If you need to see the diagnostic outputs from the mongod application these
should be available in the logfile you specified.

Cheers,

David