Merge branch 'master' into cbrain_integration

SIMEXP · May 25, 2016 · 0f791b8 · 0f791b8
2 parents dc858ab + 446887f
commit 0f791b8
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Showing 9 changed files with 41 additions and 72 deletions.
diff --git a/psom_clean.m b/psom_clean.m
@@ -77,7 +77,7 @@
 if nargin < 2
     opt = struct();
 end
-if isbool(opt)
+if islogical(opt)
     opt = struct('flag_verbose',opt);
 end
 opt = psom_struct_defaults(opt,{'flag_verbose'},{true});
@@ -127,4 +127,4 @@
     else
         warning(['I could not find the file or folder ' file_name]);
     end
-end
+end
diff --git a/psom_deamon.m b/psom_deamon.m
@@ -292,11 +292,11 @@
 
                 if (nb_resub<opt.nb_resub)||~flag_started(num_w)
                     if num_w <= opt.max_queued
-                        [flag_failed,msg] = psom_run_script(cmd_worker{num_w},script_worker{num_w},opt_worker(num_w),opt_logs_worker(num_w),opt.flag_verbose);
+                        [flag_failed,msg] = psom_run_script(cmd_worker{num_w},script_worker{num_w},opt_worker(num_w),opt_logs_worker(num_w));
                     elseif num_w == opt.max_queued+1
-                        [flag_failed,msg] = psom_run_script(cmd_pipe,script_pipe,opt_pipe,opt_logs_pipe,opt.flag_verbose);
+                        [flag_failed,msg] = psom_run_script(cmd_pipe,script_pipe,opt_pipe,opt_logs_pipe);
                     elseif num_w == opt.max_queued+2
-                        [flag_failed,msg] = psom_run_script(cmd_garb,script_garb,opt_garb,opt_logs_garb,opt.flag_verbose);
+                        [flag_failed,msg] = psom_run_script(cmd_garb,script_garb,opt_garb,opt_logs_garb);
                     end
                     if ~flag_failed
                         flag_wait(num_w) = true;
@@ -355,7 +355,7 @@
             time = clock;
             save(file_end,'time');
         end
-        sub_sleep(opt.time_between_checks)
+        pause(opt.time_between_checks)
         flag_pipe_finished = ~psom_exist(file_pipe_running);
     end
 
@@ -391,14 +391,3 @@
     end
     status_pipe = 0;
 end
-
-%%%%%%%%%%%%%%%%%%
-%% subfunctions %%
-%%%%%%%%%%%%%%%%%%
-function [] = sub_sleep(time_sleep)
-
-if exist('OCTAVE_VERSION','builtin')  
-    [res,msg] = system(sprintf('sleep %1.3f',time_sleep));
-else
-    pause(time_sleep); 
-end 
diff --git a/psom_garbage.m b/psom_garbage.m
@@ -88,7 +88,11 @@
 end
 
 %% Start heartbeat
-main_pid = getpid;
+if exist('OCTAVE_VERSION','builtin')    
+    main_pid = getpid;
+else
+    main_pid = feature('getpid');
+end
 cmd = sprintf('psom_heartbeat(''%s'',''%s'',%i)',file_heartbeat,file_kill,main_pid);
 if strcmp(gb_psom_language,'octave')
     instr_heartbeat = sprintf('"%s" %s "addpath(''%s''), %s,exit"',gb_psom_command_octave,gb_psom_opt_matlab,gb_psom_path_psom,cmd);
@@ -180,16 +184,16 @@
     end
 
     %% Update the status/logs/profile
-    save(file_logs,'-struct','-append','new_logs');
-    save(file_logs_backup,'-struct','-append','new_logs');
-    save(file_status,'-struct','-append','new_status');
-    save(file_status_backup,'-struct','-append','new_status');
-    save(file_profile,'-struct','-append','new_prof');
-    save(file_profile_backup,'-struct','-append','new_prof');
+    save(file_logs,'-append','-struct','new_logs');
+    save(file_logs_backup,'-append','-struct','new_logs');
+    save(file_status,'-append','-struct','new_status');
+    save(file_status_backup,'-append','-struct','new_status');
+    save(file_profile,'-append','-struct','new_prof');
+    save(file_profile_backup,'-append','-struct','new_prof');
 
     %% Wait if necessary
     if flag_nothing_happened && psom_exist(file_pipe_running)
-        sub_sleep(opt.time_between_checks)
+        pause(opt.time_between_checks)
 
         if (nb_checks >= opt.nb_checks_per_point)
             nb_checks = 0;
@@ -266,12 +270,3 @@
     events{num_e,1} = news_line{num_e}(1:pos-1);
     events{num_e,2} = news_line{num_e}(pos+3:end);
 end
-
-%% Work around thee 'pause' bug in octave
-function [] = sub_sleep(time_sleep)
-
-if exist('OCTAVE_VERSION','builtin')  
-    [res,msg] = system(sprintf('sleep %1.3f',time_sleep));
-else
-    pause(time_sleep); 
-end
diff --git a/psom_heartbeat.m b/psom_heartbeat.m
@@ -45,7 +45,7 @@
     if exist('OCTAVE_VERSION','builtin')  
         [err,msg] = kill(pid,0); % use the kill octave command
     else
-        [err,msg] = system(sprintf('kill %i',pid)); % kill is not available, try a system call
+        [err,msg] = system(sprintf('kill -0 %i',pid)); % kill is not available, try a system call
     end
     flag_beat = err==0;
     curr_time = clock;
@@ -64,10 +64,6 @@
         end 
         exit
     end
-    if exist('OCTAVE_VERSION','builtin')  
-        [res,msg] = system('sleep 5');
-    else
-        sleep(5); 
-    end
+    pause(5); 
 end
-
+
diff --git a/psom_manager.m b/psom_manager.m
@@ -80,7 +80,11 @@
 end
 
 %% Start heartbeat
-main_pid = getpid;
+if exist('OCTAVE_VERSION','builtin')    
+    main_pid = getpid;
+else
+    main_pid = feature('getpid');
+end
 cmd = sprintf('psom_heartbeat(''%s'',''%s'',%i)',file_heartbeat,file_kill,main_pid);
 if strcmp(gb_psom_language,'octave')
     instr_heartbeat = sprintf('"%s" %s "addpath(''%s''), %s,exit"',gb_psom_command_octave,gb_psom_opt_matlab,gb_psom_path_psom,cmd);
@@ -324,7 +328,7 @@
         %% Sleep if nothing happened
         flag_loop = (any(mask_todo) || any(mask_running)) && psom_exist(file_pipe_running) && ~psom_exist(file_pipe_end);
         if flag_nothing_happened && flag_loop
-            sub_sleep(opt.time_between_checks)
+            pause(opt.time_between_checks)
 
             if (nb_checks >= opt.nb_checks_per_point)
                 nb_checks = 0;
@@ -471,11 +475,3 @@
     fprintf('%s',str_write)
 end
 fprintf(file_write,'%s',str_write);
-
-function [] = sub_sleep(time_sleep)
-
-if exist('OCTAVE_VERSION','builtin')  
-    [res,msg] = system(sprintf('sleep %1.3f',time_sleep));
-else
-    pause(time_sleep); 
-end
diff --git a/psom_pipeline_visu.m b/psom_pipeline_visu.m
@@ -284,11 +284,7 @@
         flag_wait = ~psom_exist(file_monitor) && psom_exist(file_pipe_running);
         while flag_wait % 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');
-            if exist('OCTAVE_VERSION','builtin')  
-                [res,msg] = system('sleep 1');
-            else
-                sleep(1); 
-            end
+            pause(1); 
             flag_wait = ~psom_exist(file_monitor) && psom_exist(file_pipe_running) && (nargin<3);
         end
 

diff --git a/psom_run_pipeline.m b/psom_run_pipeline.m
@@ -505,7 +505,7 @@
 else
     script_deamon = [path_deamon filesep 'psom_deamon.sh'];
 end
-[flag_failed,msg] = psom_run_script(cmd_deamon,script_deamon,opt_script,opt_logs,opt.flag_verbose);
+[flag_failed,msg] = psom_run_script(cmd_deamon,script_deamon,opt_script,opt_logs);
 
 %% If not in session mode, monitor the output of the pipeline
 flag_exit = false;
@@ -517,11 +517,7 @@
         nb_chars_old = nb_chars;
         nb_chars = psom_pipeline_visu(opt.path_logs,'monitor',nb_chars);
         if ~any(nb_chars ~= nb_chars_old)
-            if exist('OCTAVE_VERSION','builtin')  
-                [res,msg] = system('sleep 0.2');
-            else
-                sleep(0.2); 
-            end
+            pause(0.2);
         end
     end
 end

diff --git a/psom_struct_defaults.m b/psom_struct_defaults.m
@@ -22,6 +22,7 @@
 %
 % FLAG_WARNING
 %    (boolean, default true) if FLAG_WARNING is true, issue warnings for 
+%    unrecognized fields and remove them. Otherwise do nothing about
 %    unrecognized fields.
 %
 % _________________________________________________________________________
@@ -43,8 +44,8 @@
 % i.e. they won't be copied into OPT_UP.
 %
 % Copyright (c) Pierre Bellec, Centre de recherche de l'institut de 
-% Gériatrie de Montréal, Département d'informatique et de recherche 
-% opérationnelle, Université de Montréal, 2010
+% Griatrie de Montral, Dpartement d'informatique et de recherche 
+% oprationnelle, Universit de Montral, 2010
 % Maintainer : [email protected]
 % See licensing information in the code.
 

diff --git a/psom_worker.m b/psom_worker.m
@@ -98,7 +98,11 @@
 end
 
 %% Start a heartbeat
-main_pid = getpid;
+if exist('OCTAVE_VERSION','builtin')
+    main_pid = getpid;
+else
+    main_pid = feature('getpid');
+end
 cmd = sprintf('psom_heartbeat(''%s'',''%s'',%i)',file_heartbeat,file_kill,main_pid);
 if strcmp(gb_psom_language,'octave')
     instr_heartbeat = sprintf('"%s" %s "addpath(''%s''), %s,exit"',gb_psom_command_octave,gb_psom_opt_matlab,gb_psom_path_psom,cmd);
@@ -170,7 +174,7 @@
             new_prof.time_scheduled = time_scheduled.(name_job);
             new_prof.time_running = time_running.(name_job);
             new_prof.worker = num_worker;
-            save(file_prof_job,'-struct','-append','new_prof');
+            save(file_prof_job,'-append','-struct','new_prof');
         end 
 
         test_loop = psom_exist(file_lock)&&(~flag_end||(num_job<length(list_jobs)));
@@ -180,11 +184,7 @@
         end
 
         if (num_job == length(list_jobs))&&test_loop
-            if exist('OCTAVE_VERSION','builtin')  
-                [res,msg] = system('sleep 0.1');
-            else
-                sleep(0.1); 
-            end
+            pause(0.1); 
         end
     end % While there are jobs to do
 
@@ -216,4 +216,4 @@
 else
     str_txt = fread(hf,Inf,'uint8=>char')';
     fclose(hf);    
-end
+end