general-discussion > how to use psom_gb_var
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Oct 31, 2012  09:10 AM | Alexis Machado
how to use psom_gb_var
Hi 
I would like to use the qsub mode of niak but i dont understand several elements

 I use: /data/aces/aces1/pbellec/public/niak-0.6.5c (i put it in my matlab path)

I imported the file /data/aces/aces1/pbellec/public/niak-0.6.5c/psom-717/trunk/psom_gb_vars.m into my matlab current folder in order to configure the qsub mode 

% Options for the sge qsub/msub/condor system.
gb_psom_qsub_options = '-r y -q gil.q'; 

% Options for the shell in batch, qsub, msub or condor modes
gb_psom_shell_options = ''; 

% Options for the execution mode of the pipeline 
gb_psom_mode = 'qsub'; 

% Options for the execution mode of the pipeline manager
gb_psom_mode_pm = 'batch'; 


Question 1: what should we use as gb_psom_shell_options ??

Question 2: I call my psom_gb_vars.m into my niak_preprocess.m script like this
    psom_gb_vars
    opt.psom.mode                  = 'qsub';  % Process jobs in the background
    opt.psom.mode_pipeline_manager = 'batch'; % Run the pipeline manager in the background : if I unlog, keep working
    opt.psom.max_queued            = 10;  

Do i need to configure the opt.psom fields, if yes why this redondancy ?


Question 3: we have to remove the header part of psom_gb_vars.m if we want it to work ? ( if not matlab will use gb_psom_gb_vars_local.m located in data/aces/aces1/pbellec/public/niak-0.6.5c/

%% Use the local configuration file if any
% if ~exist('gb_psom_gb_vars_local','var')&&exist('psom_gb_vars_local.m','file')
%     gb_psom_gb_vars_local = true;
%     psom_gb_vars_local
%     return
% end


Thank you very much
Best regards
Alexis