Hi Pierre, christian

I work on the BIC with the last version of NIAK, and i have issue regarding the space allowed in the /tmp folder which is limited.
I changed the tmp folder destination editing the gb_niak_tmp variable in commands/misc/niak_gb_vars.m ( /mfip/mfip1/alexis/TMP_NIAK/).

I have also edited the psom_gb_vars temporay folder to be sure to copy anything on /tmp. This file is however in my current folder ( there is another copy of psom_gb_vars) in the NIAK toolbox folder


Unfortunately i realized that NIAK continue to place some files ( not all) in the /tmp folder and at some point my pipeline crash because the /tmp is full.

 i.g: /tmp/MATLAB_Files_05-Dec-2011_11_14_52/niak_tmp_slice_timing_subject1_session1_run1_22119996CA1_MNS_BOLD_run01.dat .....
      /tmp/MATLAB_Files_05-Dec-2011_11_19_19/motion_target_subject1_session1_run2.eqsub

I have to delete these files manually, delete some
files whcih are in running and failed state in the log folder  and resume my
pipeline.


It seem that the problem occur in session and qsub mode:
Please fing my psom_gb_vars config for the qsub mode in case the source mode is involved

% 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 /data/aces/aces1/pbellec/public/niak-dev/extensions/psom/example_init_qsub.sh';

% 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