Changeset 417 for trunk/src/civ.m

Timestamp:

May 9, 2012, 6:51:16 PM (13 years ago)

Author:

g7moreau

Message:

• Change oar submit method order
• Add extra parameter for oar-parexec method
• Change stdout and stderr file extension

File:

• trunk/src/civ.m (modified) (5 diffs)

trunk/src/civ.m

@@ -1608 +1608 @@
         case 'oar'
             
-            oar_modes={'oar-dispatch','mpilauncher','oar-parexec'};
+            oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
             text={'Batch processing on servcalcul3 LEGI';...
                 'Please choose one of the followint modes';...
+                '* oar-parexec : best choice';...
                 '* oar-dispatch : jobs in a container of several cores';...
                 '* mpilauncher : one single parallel mpi job using several cores';...
-                '* oar-parexec (under development) ';...
                 '**********************************'...
                 };
@@ -1620 +1620 @@
             switch oar_modes{S}
                 case 'oar-parexec' %oar-dispatch.pl
-                    ncores=str2double(...
-                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'12'})...
-                        );
+                    answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
+                    ncores=str2double(answer{1});
+                    extra_oar=answer{2};
                     walltime_onejob=600;%seconds
                     filename_joblist=fullfile(Rootbat,'job_list.txt');
@@ -1630 +1630 @@
                     end
                     fclose(fid)
-                    oar_command=['oarsub -n test '...
-                         '-l /core=' num2str(ncores) ','...
-                        'walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
-                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
-                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
-                        '"oar-parexec -f ' filename_joblist ' -l ' filename_joblist '.log"'];
+                    oar_command=['oarsub -n CIVX '...
+                        '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
+                        '-l /core=' num2str(ncores) ','...
+                            'walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
+                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
+                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
+                        extra_oar ' '...
+                        '"oar-parexec -s -f ' filename_joblist ' '...
+                            '-l ' filename_joblist '.log"'];
                     filename_oarcommand=fullfile(Rootbat,'oar_command');
                     fid=fopen(filename_oarcommand,'w');
@@ -1651 +1654 @@
                     for p=1:length(batch_file_list)
                         oar_command=['oarsub -n CIVX '...
-                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')...
+                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
                             '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
                         fprintf(fid,[oar_command '\n']);
@@ -1659 +1662 @@
                         '-l /core=' num2str(ncores)...
                         ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
-                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
-                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
+                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
+                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
                         '"oar-dispatch -f ' filename_joblist '"'];
                     filename_oarcommand=fullfile(Rootbat,'oar_command');