- enable the use of 'list' as varargin for gtReconstructGrains (overwrites grain.rec.list)

- added the use of lists as varargin in OAR_make  (enable with oar.distribute= true)
- use these two in gtSetupReconstruction  in order to distribute the grains

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

5_reconstruction/gtReconstructGrains.m

@@ -51,6 +51,8 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
         parameters.rec.grains = rec_gr;
     end
 
+    
+    
     samplefile = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
     sample = GtSample.loadFromFile(samplefile);
 
@@ -62,7 +64,11 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
     num_grains = sample.phases{phaseID}.getNumberOfGrains();
 
     if ~isempty(rec_gr.list)
-        grains_list = rec_gr.list;
+        if isnumeric(rec_gr.list)
+            grains_list = rec_gr.list;
+        else
+            grains_list = str2num(rec_gr.list);
+        end
     else
         grains_list = first:last;
     end
@@ -70,7 +76,8 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
     % Filtering out deselected/deactivated/bad grains
     active_grains = sample.phases{phaseID}.getSelected(grains_list);
     grains_list = grains_list(active_grains);
-
+    t = GtThreshold();
+    
     fprintf('Reconstructing grains: ');
     c = tic();
     for ii = 1 : numel(grains_list)
@@ -93,14 +100,10 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
                     gtReconstructGrainOrientation(gr_id, phaseID, parameters);
                 end
         end
-
+        t.singleGrainAutoThreshold(phaseID, gr_id);
         fprintf(repmat('\b', [1 num_chars]))
     end
     fprintf('Done (in %f seconds).\n', toc(c))
-    if (isdeployed)
-        t = GtThreshold();
-        t.batchThreshold(phaseID, first, last);
-    end
 
     cd(currentDir);
 end

5_reconstruction/gtSetupReconstruction.m

@@ -142,8 +142,8 @@ if  strcmpi(check, 'y')
     end
     if (rec_on_OAR)
         launch_on_OAR('gtReconstructGrains', first, last, phaseID_str, ...
-            parameters, 'mem', 32 * 1024, 'njobs', 8, ...
-            'walltime', 3600 * 16, 'gpu', true);
+            parameters, 'core', 8, 'njobs', 8, ...
+            'walltime', 3600 * 16, 'gpu', true, 'distribute', true);
     else
         gtReconstructGrains(first, last, parameters.acq.dir, phaseID, parameters);
     end
@@ -173,11 +173,12 @@ end
 function launch_on_OAR(func_name, first, last, phaseID_str, parameters, varargin)
     disp('Launching several separate OAR jobs');
 
-    oar.njobs    = max(ceil(last/30), 30); % max 30 jobs
-    oar.walltime = last / oar.njobs * 300; % allow up to 300 seconds per grain
-    oar.mem      = 2048; % Mb
-    oar.gpu      = false;
-
+    oar.njobs      = max(ceil(last/30), 30); % max 30 jobs
+    oar.walltime   = last / oar.njobs * 300; % allow up to 300 seconds per grain
+    oar.mem        = 2048; % Mb
+    oar.gpu        = true;
+    oar.core       = 8;
+    oar.distribute = true;
     oar = parse_pv_pairs(oar, varargin);
 
     % oar parameters are defined in build_list_v2
@@ -196,8 +197,9 @@ function launch_on_OAR(func_name, first, last, phaseID_str, parameters, varargin
 
     pause(0.5);
     OAR_make(func_name, first, last, OAR_parameters.njobs, ...
-        [parameters.acq.dir ' ' phaseID_str], true, ...
+        [parameters.acq.dir ' ' phaseID_str ' '''''], true, ...
         'walltime', OAR_parameters.walltime, 'mem', OAR_parameters.mem, ...
-        'gpu', OAR_parameters.gpu);
+        'core', OAR_parameters.core, 'gpu', OAR_parameters.gpu, ...,
+        'distribute', true);
 end
 

zUtil_OAR/OAR_make.m

@@ -92,6 +92,7 @@ oarpars.checkpoint = 600;
 oarpars.signal     = 2;
 oarpars.type       = 'idempotent'; % You can also chose 'besteffort'
 oarpars.resubmit   = 0;
+oarpars.distribute = false;
 oarpars = parse_pv_pairs(oarpars, varargin);
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -218,6 +219,11 @@ set.oarparameters = strrep(set.oardirectives, '.oar', '.params');
 fid = fopen(set.oarparameters, 'w');
 
 jobsize = ceil((last-first+1)/njobs);
+
+% construct lists of grainids (will only be used when oar.distribute=true)
+for i = 1 : njobs
+    jobs{i} = [(first + i -1)  : njobs : last];
+end
 range_firsts = first:jobsize:last;
 range_lasts = range_firsts(2:end)-1;
 range_lasts(end+1) = last;
@@ -240,10 +246,17 @@ if strcmpi(func_path, m_func_path)
     end
     fprintf(fid, '# %s', help_str);
     fprintf(fid, '# \n');
-
-    for n = 1:length(range_firsts)
-        fprintf(fid, '%s %d %d %s\n', executable, range_firsts(n), ...
-                range_lasts(n), otherparameters);
+    
+    if oarpars.distribute
+        for n = 1:njobs
+            fprintf(fid, '%s %d %d %s list ''%s''\n', executable, range_firsts(n), ...
+                    range_lasts(n), otherparameters, num2str([jobs{n}]));
+        end
+    else
+        for n = 1:length(range_firsts)
+            fprintf(fid, '%s %d %d %s\n', executable, range_firsts(n), ...
+                    range_lasts(n), otherparameters);
+        end
     end
 else
     fid_tmp = fopen(func_path, 'r');