r10 - 25 Jan 2012 - 13:24:50 - FredericBastienYou are here: TWiki >  Public Web  > BramsUserGuide

Brams Users Guide

This page explain what brams user need to know about our computing environment to use the brams cluster.

If you have question, you can send them to Frédéric Bastien <nouiz@nouiz.org> and Olivier Piché <olivierpiche@gmail.com>.

Connection

To connect, you must connect by ssh to our access point and move to other computer after that.

Our access server are: {elisa1,elisa2,frontal,frontal07}.iro.umontreal.ca

elisa1 and elisa2 are the access point for our lab. frontal for the department.

frontal07 is special in that it don't block the connection that don't have a good reverse DNS. Some ISP don't implement that correctly.

please use frontal07 only if the 3 others fail.

NEVER RUN JOBS ON THOSE COMPUTER!

Cluster documentation

Our cluster documentation is at:

http://www.iro.umontreal.ca/~lisa/twiki/bin/view.cgi/Public/LisaCluster

The documentation is not very clear, so don't hesitate to contact us if you have problem.

Matlab

  • All of you should use a maximum of 6 matlab license together.
  • For now, try to coordinate this between you
  • I will try to make some more easy by the end of the year, but I can't warranty it.
  • If you need more then the 6 license, we will need our admins to find a way to use your license here.
    • This can take time, so you must plan it.
  • to be able to use spm8, you must add the path into matlab `/opt/lisa/os/matlab_toolkit/spm8`
    • as a command line: `addpath /opt/lisa/os/matlab_toolkit/spm8`
    • in the gui: File > Set Path > Add Folder
  • to be able to use Field Trip, add to your matlab path : /opt/lisa/os/matlab_toolkit/fieldtrip/

Additional point not in the documentation

  • To submit jobs to our cluster, you must do it from the zappa8 computer.
  • To run tests jobs by ssy, you must do it on the maggie46 computer. DON'T USE ZAPPA8 as this cause instability and when this happen, it can kill all running jobs...
  • To submit jobs, you must use the command jobdispatch as described in the [[http://www.iro.umontreal.ca/~lisa/twiki/bin/view.cgi/Public/LisaCluster][doc].
  • The jobs scheduler that we use is condor. jobdispatch only submit the jobs to condor and make many boiller plate work.
  • When I will have the 4 logins, I will give you priority on the brams computer.
    • to submit only on those computer, you must add the parameter `--machine=brams0{1,2,3,4,5,6,7,a,b,c,d,e,f,g}.iro.umontreal.ca` to the jobdispatch command
    • I don't plan to restrict you to only those computer but if their is problem, I will do so. (And maybe also when we have a deadline)
  • Filesystem: All files(dataset, script, executable, result) for an experiments must be under `/data/gamme/exp/$USER`.
    • If you don't do that, you will have problem with your home fileserver. The home fileserver is under NFS4 with kerberos(for security) but their is problem with Fedora 9 NFS client and the nfs server for jobs in that configuration.
    • `/data/gamme/exp/$USER` is on another computer that is NFS4 only. So we bypass some of NFS/kerberos interaction bug.
    • Also /data/gamme/exp is much faster
  • You can submit all your jobs at the same time but allow only X to run at the same time(for matlab licences, to don't overload the fileserver if that is a bottleneck in your application, to be nice...)
  • For this add the parameter `--nb_proc=X` to `jobdispatch`
  • This send 1 jobs that will act as an hyper-manager that will submit only X jobs to condor(the jobs scheduler that we use)
  • To see the currently submited jobs by this hyper-manager execute `condor_q -dag`.

-- FredericBastien - 07 Dec 2010

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