Hi
Thanks i didn't know this feature.

The problem is still here. The problem is that niak both use the /tmp and the specified tmp folder.Becuase the /tmp is limited in size , niak crash.

please find my pipeline file in attachement: you will see i have creted an if statement if i want to use session or qsub mode.


Plese find my configuration:
1-I downloaded the last verison of NIAK and installed it on mfip/mfip1/alexis/...

2-I changed the niak_gb_var.m located in the /mfip/mfip1/alexis/Sofwares/fMRI/NIAK/NIAK6.4/niak-0.6.4.1/commands/misc/niak_gb_vars.m



Please find the changes:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The following variables are needed for very fast initialization %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% where to store temporary files
% gb_niak_tmp = [filesep 'tmp' filesep];
gb_niak_tmp = ['/mfip/mfip1/alexis/TMP_NIAK' filesep];


3- I created a psom_gn_var_local.m in my current directory ( where i lauch the pipeline) that i call (psom_gn_var) when i want to execute a qsub task

Please find the changes:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The following variables need to be changed to configure the pipeline %%
%% system                                                               %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% how to invoke matlab  
gb_psom_command_matlab = '/export01/local/matlab10a/bin/matlab';

% how to invoke octave
gb_psom_command_octave = 'octave';

% Options for the sge qsub system, example : '-q all.q@yeatman,all.q@zeus'
% will force qsub to only use the yeatman and zeus workstations through the
% queue called all.q
gb_psom_qsub_options = '-r y -q grova.q';

% Options for the shell in batch or qsub modes
gb_psom_shell_options ='source /mfip/mfip1/alexis/Sofwares/fMRI/NIAK/NIAK6.4/niak-0.6.4.1/extensions/psom-0.8.8/example_init_qsub.sh';
% 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';

% Options for the maximal number of jobs
gb_psom_max_queued = 10;

% Initialization of matlab
gb_psom_init_matlab = '';

% Matlab search path. An empty value will correspond to the search path of
% the session used to invoke PSOM_RUN_PIPELINE. A value 'gb_psom_omitted'
% will result in no search path initiated (the default Octave path is
% used).
gb_psom_path_search = '';

% where to store temporary files
gb_psom_tmp = ['/mfip/mfip1/alexis/TMP_NIAK' filesep];




Best regards
Alexis