opt.mode_pipeline_manager now supports 'session', as long as opt.mode…

… is not session.

psom_deamon.m

@@ -20,6 +20,9 @@
 %      'bsub'       : remote execution using bsub (IBM)
 %      'condor'     : remote execution using condor
 %
+%   MODE_PIPELINE_MANAGER
+%      (string) same as OPT.MODE, but applies to the pipeline manager itself.
+%
 %   MAX_QUEUED
 %      (integer) The maximum number of jobs that can be processed
 %      simultaneously. Some qsub systems actually put restrictions
@@ -121,8 +124,8 @@
     opt = struct;
 end
 opt = psom_struct_defaults( opt , ...
-   {  'nb_resub' , 'flag_verbose' , 'init_matlab' , 'shell_options' , 'command_matlab' , 'mode' , 'max_queued' , 'max_buffer' , 'qsub_options' , 'time_between_checks' , 'nb_checks_per_point' }, ...
-   {  NaN        , 1              , NaN           , NaN             , NaN              , NaN    , NaN          , NaN          , NaN            , NaN                   , NaN                   });
+   {  'mode_pipeline_manager' , 'nb_resub' , 'flag_verbose' , 'init_matlab' , 'shell_options' , 'command_matlab' , 'mode' , 'max_queued' , 'max_buffer' , 'qsub_options' , 'time_between_checks' , 'nb_checks_per_point' }, ...
+   {  NaN                     , NaN        , 1              , NaN           , NaN             , NaN              , NaN    , NaN          , NaN          , NaN            , NaN                   , NaN                   });
 
 if ~strcmp(path_logs(end),filesep)
     path_logs = [path_logs filesep];
@@ -172,6 +175,7 @@
     nb_resub    = 0;                   % Number of resubmission               
     nb_checks   = 0;                   % Number of checks to print a points
     nb_points   = 0;                   % Number of printed points
+    nb_chars_logs = 0;                 % Number of characters printed from the pipeline history                
     flag_pipe_running  = false;        % Is the pipeline started?
     flag_pipe_finished = false;        % Is the pipeline finished?
     flag_started = false([opt.max_queued+2 1]); % Has the worker ever started? two last entries are for the PM and the GC
@@ -236,12 +240,12 @@
         opt_logs_worker(num_w).failed = sprintf('%spsom%i%sworker.failed',path_worker,num_w,filesep);
         opt_logs_worker(num_w).exit   = sprintf('%spsom%i%sworker.exit',path_worker,num_w,filesep);   
         opt_worker(num_w) = opt_script;
-        opt_worker(num_w).name_job = sprintf('psom%i',num_w);   
+        opt_worker(num_w).name_job = name_worker{num_w};
         cmd_worker{num_w} = sprintf('flag.heartbeat = true; flag.spawn = true; psom_worker(''%s'',flag);',path_worker_w{num_w});
         if ispc % this is windows
-            script_worker{num_w} = [path_tmp filesep opt_worker.name_job '.bat'];
+            script_worker{num_w} = [path_tmp filesep opt_worker(num_w).name_job '.bat'];
         else
-            script_worker{num_w} = [path_tmp filesep opt_worker.name_job '.sh'];
+            script_worker{num_w} = [path_tmp filesep opt_worker(num_w).name_job '.sh'];
         end
     end
 
@@ -363,7 +367,14 @@
                 end
             end
         end
-        sub_sleep(opt.time_between_checks*10)
+        if ~strcmp(opt.mode_pipeline_manager,'session')
+            sub_sleep(opt.time_between_checks*10)
+        else
+            if opt.flag_verbose
+                nb_chars_logs = psom_pipeline_visu(path_logs,'monitor',nb_chars_logs);
+            end
+            sub_sleep(opt.time_between_checks)
+        end
         flag_pipe_finished = ~psom_exist(file_pipe_running);
     end
 

psom_pipeline_init.m

@@ -951,7 +951,7 @@ function sub_save_struct_fields(file_name,var_struct,flag_append)
         pipeline_str = load(file_name);
     catch
         [path_f,name_f,ext_f] = fileparts(file_name);
-        file_backup = [path_f name_f '_backup' ext_f];
+        file_backup = [path_f filesep name_f '_backup' ext_f];
         warning('There was something wrong when loading the file %s, I''ll try loading the backup instead',file_name)
         pipeline_str = load(file_backup);
         copyfile(file_backup,file_name,'f');

psom_pipeline_visu.m

@@ -121,9 +121,9 @@
 %
 % Copyright (c) Pierre Bellec, 
 % Montreal Neurological Institute, 2008-2010
-% Département d'informatique et de recherche opérationnelle
-% Centre de recherche de l'institut de Gériatrie de Montréal
-% Université de Montréal, 2011
+% Dpartement d'informatique et de recherche oprationnelle
+% Centre de recherche de l'institut de Griatrie de Montral
+% Universit de Montral, 2011
 % Maintainer : [email protected]
 % See licensing information in the code.
 % Keywords : pipeline
@@ -236,24 +236,22 @@
         file_monitor = [path_logs filesep name_pipeline '_history.txt'];
         file_pipe_running = [path_logs filesep name_pipeline '.lock'];
 
-        if exist(file_pipe_running,'file')
-            msg = 'The pipeline is currently running';
-        else
-            msg = 'The pipeline is NOT currently running';
+        if ~psom_exist(file_pipe_running)
+            fprintf('The pipeline is NOT currently running\n');
         end
-
-        stars = repmat('*',size(msg));
-        fprintf('\n\n%s\n%s\n%s\n\n',stars,msg,stars);
-
+
         while ~psom_exist(file_monitor) && psom_exist(file_pipe_running) % the pipeline started but the log file has not yet been created
 
             fprintf('I could not find any log file. This pipeline has not been started (yet?). Press CTRL-C to cancel.\n');
             pause(1)
 
         end
 
-        sub_tail(file_monitor,file_pipe_running,opt_action);
-        res = [];
+        if nargin<3
+            res = sub_tail(file_monitor,file_pipe_running,opt_action);
+        else 
+            res = sub_read_update(file_monitor,opt_action);
+        end
 
     case 'time'
 
@@ -440,7 +438,17 @@
 %% sub-functions %%
 %%%%%%%%%%%%%%%%%%%
 
-function [] = sub_tail(file_read,file_running,nb_chars)
+function nb_chars = sub_read_update(file_read,nb_chars)
+
+% prints out update on FILE_READ 
+hf = fopen(file_read,'r');
+fseek(hf,nb_chars,'bof');
+str_read = fread(hf, Inf , 'uint8=>char')';
+nb_chars = ftell(hf);
+fclose(hf);    
+fprintf('%s',str_read);            
+
+function nb_chars = sub_tail(file_read,file_running)
 
 % prints out the content of the text file FILE_READ with constant updates
 % as long as the file FILE_RUNNING exists. 

psom_run_pipeline.m

@@ -394,8 +394,7 @@
 
 %% Run the pipeline manager
 file_pipeline = cat(2,opt.path_logs,filesep,name_pipeline,'.mat');
-if strcmp(opt.mode_pipeline_manager,'session')
-else
+if 0==0
 
     %% Create a folder for the PSOM deamon
     path_deamon = [opt.path_logs 'deamon' filesep];
@@ -406,6 +405,7 @@
 
     %% The options for the deamon
     opt_d.mode           = opt.mode;
+    opt_d.mode_pipeline_manager = opt.mode_pipeline_manager;
     opt_d.max_queued     = opt.max_queued;
     opt_d.max_buffer     = opt.max_buffer;
     opt_d.nb_resub       = opt.nb_resub;
@@ -446,5 +446,8 @@
 
 %% If not in session mode, monitor the output of the pipeline
 if opt.flag_verbose&&~strcmp(opt.mode_pipeline_manager,'session')
-    psom_pipeline_visu(opt.path_logs,'monitor',0);
+    nb_chars = 0;
+    while (nb_chars==0)||psom_exist(file_pipe_running)
+        nb_chars = psom_pipeline_visu(opt.path_logs,'monitor',nb_chars);
+    end
 end

psom_run_script.m

@@ -301,26 +301,16 @@
 
     case 'session'
 
-        try
-            if ~isempty(logs)
-                diary(logs.txt);
-                sub_eval(cmd);
-                diary off;
-            else
-                sub_eval(cmd);
-            end
-            flag_failed = false;
-            msg = '';
-        catch
-            flag_failed = true;
-            errmsg = lasterror;
-            msg = errmsg.message;
-            if isfield(errmsg,'stack')
-                for num_e = 1:length(errmsg.stack)
-                    msg = sprintf('%s\nFile %s at line %i\n',msg,errmsg.stack(num_e).file,errmsg.stack(num_e).line);
-                end           
-            end
+        if ~isempty(logs)
+            diary(logs.txt);
+            sub_eval(cmd);
+            diary off;
+        else
+            sub_eval(cmd);
         end
+        flag_failed = false;
+        msg = '';
+
         if ~isempty(logs.exit)
             save(logs.exit,'flag_failed')
         end
@@ -418,7 +408,12 @@
 end
 
 if (flag_failed~=0)&&exist('errmsg','var')
-    fprintf('\n    The execution of the job %s failed.\n The feedback was : %s\n',opt.name_job,errmsg);
+    fprintf('\n    The execution of the job %s failed.\n The feedback was:\n',opt.name_job);
+    if isfield(errmsg,'stack')
+        for num_e = 1:length(errmsg.stack)
+            fprintf('File %s at line %i\n',errmsg.stack(num_e).file,errmsg.stack(num_e).line);
+        end
+    end
 elseif (flag_failed==0)&&exist('errmsg','var')&&opt.flag_debug
     fprintf('\n    The feedback from the execution of job %s was : %s\n',opt.name_job,errmsg);
 end