general-discussion > how to use psom_gb_var
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Oct 31, 2012 04:10 PM | 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
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