Setting up MongoDB in High Performance Computing LSF linux cluster

Posted by Dnaiel on Server Fault See other posts from Server Fault or by Dnaiel
Published on 2012-10-03T01:41:04Z Indexed on 2012/10/03 21:42 UTC
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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.

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