Psom with docker agent not tested but all is there

docker_psom_worker_submit.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+# Script config
+# docker command
+DOCKER_EXE=docker
+# docker options DEFAULT: " -v $HOME:$HOME --user $UID "
+DOCKER_OPTIONS=" -v $HOME:$HOME --user $UID "
+# image that docker will use to run agent, image is pulled before it is run.
+DOCKER_IMAGE=simexp/niak-boss:latest
+# Worker init script
+WORKER_INIT_SCRIPT=psom_worker.py
+
+
+if [ $# != 2 ]
+then
+    echo "usage: $0 <psom_dir> <output_dir> <worker_id>"
+    exit 1
+fi
+
+PSOM_DIR=$1s
+OUTPUT_DIR=$2
+WORKER_ID=$3
+
+
+${DOCKER_EXE} pull ${DOCKER_IMAGE}
+${DOCKER_EXE} run --rm ${DOCKER_OPTIONS} ${DOCKER_IMAGE} \
+    /bin/bash -lic "${PSOM_DIR}/${WORKER_INIT_SCRIPT} -d ${OUTPUT_DIR} -w ${WORKER_ID}"

psom_config.m

@@ -139,7 +139,7 @@
     end
 end
 
-if ~ismember(opt.mode,{'session','background','batch','qsub','msub','condor','cbrain'})
+if ~ismember(opt.mode,{'session','background','batch','qsub','msub','condor','cbrain','docker'})
     error('%s is an unknown mode of pipeline execution. Sorry dude, I must quit ...',opt.mode);
 end
 

psom_gb_vars.m

@@ -27,11 +27,11 @@
 gb_psom_shell_options = ''; 
 
 % Options for the execution mode of the pipeline 
-%gb_psom_mode = 'session'; 
-gb_psom_mode = 'background'; 
+gb_psom_mode = 'session'; 
+%gb_psom_mode = 'background'; 
 
 % Options for the execution mode of the pipeline manager
-gb_psom_mode_pm = 'background'; 
+gb_psom_mode_pm = 'session'; 
 
 % Options for the execution mode of the deamon
 gb_psom_mode_deamon = 'background'; 

psom_gb_vars_local.m

@@ -30,6 +30,7 @@
 gb_psom_shell_options = ''; 
 
 % Options for the execution mode of the pipeline 
+%gb_psom_mode = 'docker';
 gb_psom_mode = 'cbrain';
 % gb_psom_mode = 'cbrain_psom_agent_start';
 

psom_run_pipeline.m

@@ -374,7 +374,7 @@
 % Limit the number of workers based on the number of jobs in the pipeline
 opt.max_queued = min(opt.max_queued,length(fieldnames(pipeline)));
 
-if ~ismember(opt.mode,{'session','background','batch','qsub','msub','bsub','condor','cbrain'})
+if ~ismember(opt.mode,{'session','background','batch','qsub','msub','bsub','condor','cbrain','docker'})
     error('%s is an unknown mode of pipeline execution. Sorry dude, I must quit ...',opt.mode);
 end
 

psom_run_script.m

@@ -175,6 +175,7 @@
 list_fields    = { 'flag_short_job_names' , 'path_search'       , 'file_handle' , 'name_job'    , 'init_matlab'       , 'flag_debug' , 'shell_options'       , 'command_matlab' , 'mode' , 'qsub_options'       };
 list_defaults  = { true                   , gb_psom_path_search , []            , 'psom_script' , gb_psom_init_matlab , false        , gb_psom_shell_options , ''               , NaN    , gb_psom_qsub_options };
 opt = psom_struct_defaults(opt,list_fields,list_defaults);
+
 if opt.flag_debug
     msg = sprintf('\n    The execution mode is %s\n',opt.mode);
     fprintf(msg);
@@ -204,7 +205,7 @@
     logs = [];
 else
     list_fields   = { 'txt' , 'eqsub' , 'oqsub' , 'failed' , 'exit' };
-    if ismember(opt.mode,{'qsub','msub','bsub','condor','cbrain'})
+    if ismember(opt.mode,{'qsub','msub','bsub','condor','cbrain','docker'})
         list_defaults = { NaN   , NaN     , NaN     , NaN    , ''     };
     else
         list_defaults = { NaN   , ''      , ''      , ''     , ''     };
@@ -213,7 +214,7 @@
 end
 
 %% Check that the execution mode exists
-if ~ismember(opt.mode,{'session','background','batch','qsub','msub','bsub','condor','cbrain'})
+if ~ismember(opt.mode,{'session','background','batch','qsub','msub','bsub','condor','cbrain','docker'})
     error('%s is an unknown mode of command execution. Sorry dude, I must quit ...',opt.mode);
 end
 
@@ -306,7 +307,7 @@
         else
             sub_eval(cmd);
         end
-        flag_failed = false;
+        flag_failed = 0;
         msg = '';
 
         if ~isempty(logs.exit)
@@ -400,24 +401,65 @@
     case {'cbrain'}
 
         sub = [gb_psom_path_psom 'cbrain_psom_worker_submit.sh'];
+        % There might be a better way to find the job path and id, 
+        % however, I do not know the code well
+        % enough at that point.
+        result_path = regexp(script,'(^.*)/logs','tokens'){1}{1};
+        agent_id = regexp(script,'psom_*(\w*)','tokens'){1}{1};
+        instr_cbrain = sprintf('%s %s %s', sub, result_path, agent_id);
+
+        if opt.flag_debug
+            if strcmp(gb_psom_language,'octave')
+                % In octave, the error stream is lost. Redirect it to standard output
+                instr_cbrain = [instr_cbrain ' 2>&1'];
+            end
+            msg = sprintf('    The script is executed using the command :\n%s\n\n',instr_qsub);
+            fprintf('%s',msg);
+            if ~isempty(opt.file_handle)
+                fprintf(opt.file_handle,'%s',msg);
+            end
+
+        end
+        fprintf(1,'%s \n',instr_cbrain);
+        [flag_failed,msg] = system(instr_cbrain)
+
+    case {'docker'}
+
+        sub=['qsub']
+        script = [gb_psom_path_psom 'run_in_docker.sh'];
         % There might be a better way to find the job path and id, however, I do not know the code well
         %  enough at that point.
-        le_path = regexp(script,'(^.*)/logs','tokens'){1}{1};
-        le_id = regexp(script,'psom_*(\w*)','tokens'){1}{1};
-        instr_cbrain = sprintf('%s %s %s',sub,le_path,le_id);
+        result_path = regexp(script,'(^.*)/logs','tokens'){1}{1};
+        agent_id = regexp(script,'psom_*(\w*)','tokens'){1}{1};
+
+        if ~isempty(logs)
+            qsub_logs = [' -e \"' logs.eqsub '\" -o \"' logs.oqsub '\"'];
+        else
+            qsub_logs = '';
+        end
+        if opt.flag_short_job_names
+            name_job = opt.name_job(1:min(length(opt.name_job),8));
+        else
+            name_job = opt.name_job;
+        end
+
+        instr_qsub_docker = sprintf('%s %s -N %s %s %s', sub, qsub_logs, name_job, opt.qsub_options ...
+                             , ['\"' script, gb_psom_path_psom, result_path, agent_id '\"']);
 
         if opt.flag_debug
             if strcmp(gb_psom_language,'octave')
-                instr_cbrain = [instr_qsub ' 2>&1']; % In octave, the error stream is lost. Redirect it to standard output
+                % In octave, the error stream is lost. Redirect it to standard output
+                instr_qsub_docker = [instr_qsub_docker ' 2>&1'];
             end
-            msg = sprintf('    The script is executed using the command :\n%s\n\n',instr_qsub);
+            msg = sprintf('  The script is executed using the command :\n%s\n\n',instr_qsub);
             fprintf('%s',msg);
             if ~isempty(opt.file_handle)
                 fprintf(opt.file_handle,'%s',msg);
             end
+
         end
-         fprintf(1,'%s \n',instr_cbrain);
-         [flag_failed,msg] = system(instr_cbrain);
+        fprintf(1,'%s \n', instr_qsub_docker);
+        [flag_failed,msg] = system(instr_qsub_docker)
 
 end