Changeset 918
- Timestamp:
- Jun 26, 2015, 9:20:48 AM (9 years ago)
- Location:
- trunk/src
- Files:
-
- 4 edited
-
series.m (modified) (8 diffs)
-
series/civ_input.m (modified) (7 diffs)
-
set_grid.fig (modified) (previous)
-
set_grid.m (modified) (5 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/src/series.m
r917 r918 1480 1480 end 1481 1481 1482 %% Get RunTime code from the file PARAM.xml (needed to run compiled functions)1482 %% Get PARAM.xml (not used at this stage) 1483 1483 errormsg='';%default error message 1484 1484 xmlfile=fullfile(path_series,'PARAM.xml'); … … 1761 1761 '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n']) 1762 1762 RunMode = 'python'; 1763 t = struct2xml(Param);1764 t = set(t, 1, 'name', 'Series');1765 filexml = fullfile_uvmat(DirXml, '', Param.InputTable{1,3}, '.xml', OutputNomType,...1766 Param.IndexRange.first_i, Param.IndexRange.last_i, first_j, last_j);1767 save(t, filexml);1768 1763 end 1769 1764 1770 1765 1771 1766 %% direct processing on the current Matlab session 1772 if strcmp (RunMode,'local') 1773 for iprocess=1:NbProcess 1774 if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action 1775 disp('program stopped by user') 1776 return 1777 end 1778 if isempty(Param.IndexRange.NbSlice) 1779 %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; 1780 Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); 1781 if Param.IndexRange.first_i>last_i 1782 break 1783 end 1784 Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i); 1785 %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i); 1786 else %multislices (then incr_i is not empty) 1787 Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); 1788 Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; 1789 end 1790 if isfield(Param,'OutputSubDir') 1791 t=struct2xml(Param); 1792 t=set(t,1,'name','Series'); 1793 filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,... 1794 Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); 1795 save(t,filexml); 1796 end 1767 % if strcmp (RunMode,'local') 1768 for iprocess=1:NbProcess 1769 if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action 1770 disp('program stopped by user') 1771 return 1772 end 1773 if isempty(Param.IndexRange.NbSlice) 1774 Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; 1775 % Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); 1776 if Param.IndexRange.first_i>last_i 1777 NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation 1778 break 1779 end 1780 %Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i); 1781 %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i); 1782 Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); 1783 else %multislices (then incr_i is not empty) 1784 % Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); 1785 % Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; 1786 Param.IndexRange.first_i= first_i+iprocess-1; 1787 Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; 1788 end 1789 for ilist=1:size(Param.InputTable,1) 1790 Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system 1791 end 1792 1793 % if isempty(Param.IndexRange.NbSlice)% process by blocks of i index 1794 % Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; 1795 % if Param.IndexRange.first_i>last_i 1796 % NbProcess=iprocess-1; 1797 % break% leave the loop, we are at the end of the calculation 1798 % end 1799 % Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); 1800 % else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1 1801 % Param.IndexRange.first_i= first_i+iprocess-1; 1802 % Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; 1803 % end 1804 1805 1806 if isfield(Param,'OutputSubDir') 1807 t=struct2xml(Param); 1808 t=set(t,1,'name','Series'); 1809 extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,... 1810 Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); 1811 filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}) 1812 save(t, filexml{iprocess});% save the xml file containing the processing parameters 1813 end 1814 if strcmp (RunMode,'local') 1797 1815 switch ActionExt 1798 1816 case '.m' 1799 h_fun(Param); 1817 h_fun(Param);% direct launching 1800 1818 case '.sh' 1801 1819 switch computer … … 1808 1826 end 1809 1827 end 1810 elseif ~strcmp(RunMode,'python') 1828 end 1829 if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') 1811 1830 %% processing on a different session of the same computer (background) or cluster, create executable files 1812 1831 batch_file_list=cell(NbProcess,1);% initiate the list of executable files … … 1835 1854 end 1836 1855 end 1856 %create the executable file 1857 file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,... 1858 first_i,last_i,first_j,last_j); 1859 file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global); 1860 filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,... 1861 first_i,last_i,first_j,last_j); 1862 filelog_global=fullfile(OutputDir,'0_LOG',filelog_global); 1863 1864 1837 1865 for iprocess=1:NbProcess 1838 if isempty(Param.IndexRange.NbSlice)% process by blocks of i index1839 Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;1840 if Param.IndexRange.first_i>last_i1841 NbProcess=iprocess-1;1842 break% leave the loop, we are at the end of the calculation1843 end1844 Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);1845 else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =11846 Param.IndexRange.first_i= first_i+iprocess-1;1847 Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;1848 end1849 for ilist=1:size(Param.InputTable,1)1850 Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system1851 end1852 % create, fill and save the xml parameter file1853 t=struct2xml(Param);1854 t=set(t,1,'name','Series');1855 filexml{iprocess}=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...1856 Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);1857 save(t,filexml{iprocess});% save the parameter file1858 1866 1867 %create the executable file 1868 1869 batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); 1870 % [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file 1871 % if isequal(fid,-1) 1872 % errormsg=['creation of ' batch_file_list{iprocess} ':' message]; 1873 % return 1874 % end 1859 1875 1860 1876 % set the log file name 1861 filelog{iprocess}=fullfile _uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...1862 Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);1877 filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log')); 1878 1863 1879 end 1864 1880 end 1865 1881 1866 1882 %% launch the executable files for background or cluster processing 1883 1867 1884 switch RunMode 1885 1868 1886 case 'background' 1869 % create the executable file 1870 filebat=fullfile_uvmat(DirExe,'',Param.InputTable{1,3},ExeExt,OutputNomType,... 1871 first_i,last_i,first_j,last_j); 1872 %batch_file_list{iprocess}=filebat; 1873 [fid,message]=fopen(filebat,'w');% create the executable file 1887 [fid,message]=fopen(file_exe_global,'w'); 1874 1888 if isequal(fid,-1) 1875 errormsg=['creation of .bat file:' message];1889 errormsg=['creation of ' file_exe_global ':' message]; 1876 1890 return 1877 1891 end 1878 filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...1879 first_i,last_i,first_j,last_j);1880 1892 switch ActionExt 1881 1893 case '.m'% Matlab function … … 1885 1897 '#!/bin/bash \n'... 1886 1898 '. /etc/sysprofile \n'... 1887 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...1899 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB \n'... 1888 1900 'addpath(''' path_series '''); \n'... 1889 1901 'addpath(''' Param.Action.ActionPath '''); \n']; … … 1894 1906 fprintf(fid,cmd);%fill the executable file with the char string cmd 1895 1907 fclose(fid);% close the executable file 1896 system(['chmod +x ' file bat]);% set the file to executable1908 system(['chmod +x ' file_exe_global]);% set the file to executable 1897 1909 case {'PCWIN','PCWIN64'} 1898 1910 cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')... … … 1900 1912 'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');']; 1901 1913 for iprocess=1:NbProcess 1902 cmd=[cmd '' Param.Action.ActionName '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');'] 1914 cmd=[cmd '' Param.Action.ActionName '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');'] 1903 1915 end 1904 1916 cmd=[cmd ';exit"']; … … 1906 1918 fclose(fid);% close the executable file 1907 1919 end 1908 system([file bat ' &'])% directly execute the command file1920 system([file_exe_global ' &'])% directly execute the command file 1909 1921 case '.sh' % compiled Matlab function 1910 switch computer 1911 case {'GLNX86','GLNXA64','MACI64'} 1912 cmd=['#!/bin/bash \n '... 1913 '#$ -cwd \n '... 1914 'sleep $(( $RANDOM / 3000 )) \n '... 1915 'hostname && date \n '... 1916 'umask 002 \n'] 1917 for iprocess=1:NbProcess 1918 cmd=[cmd fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group 1919 end 1920 fprintf(fid,cmd);%fill the executable file with the char string cmd 1921 fclose(fid);% close the executable file 1922 system(['chmod +x ' filebat]);% set the file to executable 1923 system([filebat ' &'])% directly execute the command file 1924 case {'PCWIN','PCWIN64'} 1925 msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system') 1926 return 1922 for iprocess=1:NbProcess 1923 switch computer 1924 case {'GLNX86','GLNXA64','MACI64'} 1925 [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file 1926 if isequal(fid,-1) 1927 errormsg=['creation of .bat file: ' message]; 1928 return 1929 end 1930 cmd=['#!/bin/bash \n '... 1931 '#$ -cwd \n '... 1932 'hostname && date \n '... 1933 'umask 002 \n'... 1934 fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group 1935 fprintf(fid,cmd);%fill the executable file with the char string cmd 1936 fclose(fid);% close the executable file 1937 system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable 1938 system([batch_file_list{iprocess} ' &'])% directly execute the command file 1939 case {'PCWIN','PCWIN64'} 1940 msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system') 1941 return 1942 end 1927 1943 end 1928 1944 msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results']) 1929 case 'cluster_oar' % option 'oar-parexec' used 1930 %create subdirectory for oar command and global log files 1931 DirOAR=fullfile(OutputDir,'0_OAR'); 1932 if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input 1933 curdir=pwd; 1934 cd(DirOAR) 1935 delete('*') 1936 cd(curdir) 1937 else 1938 [tild,msg1]=mkdir(DirOAR); 1939 if ~strcmp(msg1,'') 1940 errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation 1941 return 1942 end 1943 end 1944 filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file 1945 filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process 1946 filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process 1947 1948 fid=fopen(filename_joblist,'w'); 1949 for p=1:length(batch_file_list) 1950 fprintf(fid,[batch_file_list{p} '\n']);% list of exe files 1951 end 1952 fclose(fid); 1953 system(['chmod +x ' filename_joblist]);% set the file to executable 1954 1955 % the command job_list.txt contains the list of NbProcess independent individual jobs 1956 % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE. 1957 % These individual jobs are grouped by the system as oar jobs on the NbCore processors. 1958 % For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h. 1959 % However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are 1960 % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration, 1961 % the oar job restarts when an individual job ends. 1962 JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes) 1963 % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h: 1964 WallTimeTotal=min(23,4*JobTime/60); 1965 %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours']) 1966 % estimated time of an individual job (in min), with a margin of error 1967 WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint 1968 disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes']) 1969 oar_command=['oarsub -n UVmat_' ActionName ' '... 1970 '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '... 1971 '-l /core=' num2str(NbCore) ','... 1972 'walltime=' datestr(WallTimeTotal/24,13) ' '... 1973 '-E ' filename_errors ' '... 1974 '-O ' filename_log ' '... 1975 extra_oar ' '... 1976 '"oar-parexec -s -f ' filename_joblist ' '... 1977 '-l ' filename_joblist '.log"']; 1978 fprintf(oar_command);% display system command on the Matlab command window 1979 [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window 1980 filename_oarcommand=fullfile(DirOAR,'0_oar_command');% keep track of the command in file '0-OAR/0_oar_command' 1981 fid=fopen(filename_oarcommand,'w'); 1982 fprintf(fid,oar_command); % store the command 1983 fprintf(fid,result);% store the result (job ID number) 1984 fclose(fid); 1985 1986 msgbox_uvmat('CONFIRMATION',[ActionName ' launched as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) 1987 case 'cluster_pbs' % for LMFA Kepler machine 1988 %create subdirectory for pbs command and log files 1989 DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS 1990 if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input 1991 curdir=pwd; 1992 cd(DirPBS) 1993 delete('*') 1994 cd(curdir) 1995 else 1996 [tild,msg1]=mkdir(DirPBS); 1997 if ~strcmp(msg1,'') 1998 errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation 1999 return 2000 end 2001 end 2002 max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h) 2003 walltime_onejob=1800; % seconds, max estimated time for asingle file index value 2004 filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file 2005 fid=fopen(filename_joblist,'w'); 2006 for p=1:length(batch_file_list) 2007 fprintf(fid,[batch_file_list{p} '\n']);% list of exe files 2008 end 2009 fclose(fid); 2010 system(['chmod +x ' filename_joblist]);% set the file to executable 2011 pbs_command=['qstat -n CIVX '... 2012 '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... 2013 '-l /core=' num2str(NbCore) ','... 2014 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '... 2015 '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... 2016 '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '... 2017 extra_oar ' '... 2018 '"oar-parexec -s -f ' filename_joblist ' '... 2019 '-l ' filename_joblist '.log"']; 2020 filename_oarcommand=fullfile(DirPBS,'pbs_command'); 2021 fid=fopen(filename_oarcommand,'w'); 2022 fprintf(fid,pbs_command); 2023 fclose(fid); 2024 fprintf(pbs_command);% display in command line 2025 %system(pbs_command); 2026 msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster']) 2027 case 'python' 2028 command = [ 2029 'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ... 2030 'python -m fluiddyn.postproc.uvmat ' filexml{iprocess}]; 2031 % fprintf(['command:\n' command '\n\n']) 2032 system(command, '-echo'); 2033 end 2034 end 1945 end 1946 1947 case 'cluster_oar' % option 'oar-parexec' used 1948 %create subdirectory for oar commands 1949 for iprocess=1:NbProcess 1950 [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file 1951 if isequal(fid,-1) 1952 errormsg=['creation of .bat file: ' message]; 1953 return 1954 end 1955 if strcmp(ActionExt,'.sh') 1956 cmd=['#!/bin/bash \n '... 1957 '#$ -cwd \n '... 1958 'hostname && date \n '... 1959 'umask 002 \n'... 1960 fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group 1961 else 1962 cmd=[... 1963 '#!/bin/bash \n'... 1964 '. /etc/sysprofile \n'... 1965 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog{iprocess} ''' <<END_MATLAB \n'... 1966 'addpath(''' path_series '''); \n'... 1967 'addpath(''' Param.Action.ActionPath '''); \n'... 1968 '' Param.Action.ActionName '( ''' filexml{iprocess} '''); \n'... 1969 'exit \n'... 1970 'END_MATLAB \n']; 1971 end 1972 fprintf(fid,cmd);%fill the executable file with the char string cmd 1973 fclose(fid);% close the executable file 1974 system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable 1975 end 1976 DirOAR=fullfile(OutputDir,'0_OAR'); 1977 if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input 1978 curdir=pwd; 1979 cd(DirOAR) 1980 delete('*') 1981 cd(curdir) 1982 else 1983 [tild,msg1]=mkdir(DirOAR); 1984 if ~strcmp(msg1,'') 1985 errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation 1986 return 1987 end 1988 end 1989 % create file containing the list of jobs 1990 filename_joblist=fullfile(DirOAR,'job_list.txt');% name of the file contqining the list of executables 1991 fid=fopen(filename_joblist,'w');%open it for writting 1992 for iprocess=1:length(batch_file_list) 1993 fprintf(fid,[batch_file_list{iprocess} '\n']);% write list of exe files 1994 end 1995 fclose(fid); 1996 system(['chmod +x ' filename_joblist]);% set the file to executable 1997 1998 filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process 1999 filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process 2000 % the command job_list.txt contains the list of NbProcess independent individual jobs 2001 % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE. 2002 % These individual jobs are grouped by the system as oar jobs on the NbCore processors. 2003 % For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h. 2004 % However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are 2005 % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration, 2006 % the oar job restarts when an individual job ends. 2007 JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes) 2008 % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h: 2009 WallTimeTotal=min(23,4*JobTime/60); 2010 %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours']) 2011 % estimated time of an individual job (in min), with a margin of error 2012 WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint 2013 disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes']) 2014 oar_command=['oarsub -n UVmat_' ActionName ' '... 2015 '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '... 2016 '-l /core=' num2str(NbCore) ','... 2017 'walltime=' datestr(WallTimeTotal/24,13) ' '... 2018 '-E ' filename_errors ' '... 2019 '-O ' filename_log ' '... 2020 extra_oar ' '... 2021 '"oar-parexec -s -f ' filename_joblist ' '... 2022 '-l ' filename_joblist '.log"']; 2023 fprintf(oar_command);% display system command on the Matlab command window 2024 [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window 2025 filename_oarcommand=fullfile(DirOAR,'0_oar_command');% keep track of the command in file '0-OAR/0_oar_command' 2026 fid=fopen(filename_oarcommand,'w'); 2027 fprintf(fid,oar_command); % store the command 2028 fprintf(fid,result);% store the result (job ID number) 2029 fclose(fid); 2030 msgbox_uvmat('CONFIRMATION',[ActionName ' launched as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) 2031 2032 case 'cluster_pbs' % for LMFA Kepler machine 2033 %create subdirectory for pbs command and log files 2034 DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS 2035 if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input 2036 curdir=pwd; 2037 cd(DirPBS) 2038 delete('*') 2039 cd(curdir) 2040 else 2041 [tild,msg1]=mkdir(DirPBS); 2042 if ~strcmp(msg1,'') 2043 errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation 2044 return 2045 end 2046 end 2047 max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h) 2048 walltime_onejob=1800; % seconds, max estimated time for asingle file index value 2049 filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file 2050 fid=fopen(filename_joblist,'w'); 2051 for iprocess=1:length(batch_file_list) 2052 fprintf(fid,[batch_file_list{iprocess} '\n']);% list of exe files 2053 end 2054 fclose(fid); 2055 system(['chmod +x ' filename_joblist]);% set the file to executable 2056 pbs_command=['qstat -n CIVX '... 2057 '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... 2058 '-l /core=' num2str(NbCore) ','... 2059 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '... 2060 '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... 2061 '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '... 2062 extra_oar ' '... 2063 '"oar-parexec -s -f ' filename_joblist ' '... 2064 '-l ' filename_joblist '.log"']; 2065 filename_oarcommand=fullfile(DirPBS,'pbs_command'); 2066 fid=fopen(filename_oarcommand,'w'); 2067 fprintf(fid,pbs_command); 2068 fclose(fid); 2069 fprintf(pbs_command);% display in command line 2070 %system(pbs_command); 2071 msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster']) 2072 case 'python' 2073 command = [ 2074 'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ... 2075 'python -m fluiddyn.postproc.uvmat ' filexml{iprocess}]; 2076 % fprintf(['command:\n' command '\n\n']) 2077 system(command, '-echo'); 2078 end 2079 2035 2080 %------------------------------------------------------------------------ 2036 2081 function STOP_Callback(hObject, eventdata, handles) -
trunk/src/series/civ_input.m
r910 r918 207 207 end 208 208 end 209 if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs 210 set(handles.ListPairMode,'Value',1) 211 set(handles.ListPairMode,'String',{'series(Di)'}) 212 elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j 213 set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) 214 if MaxIndex_j <= 10 215 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large 216 end 217 else 218 set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice 219 if strcmp(NomTypeNc,'_1-2_1') 220 set(handles.ListPairMode,'Value',3)% advise 'series(Di)' 221 elseif MaxIndex_j <= 10 222 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large 223 end 224 end 209 225 210 226 211 %% transfer the time from the GUI series, or use file index by default … … 272 257 %set(handles.CoordUnit,'String',CoordUnit) 273 258 set(handles.SearchRange,'UserData', pxcm_search); 274 275 % indicate the min and max indices i and j on the GUI276 set(handles.MinIndex_i,'String',num2str(MinIndex_i))277 set(handles.MaxIndex_i,'String',num2str(MaxIndex_i))278 set(handles.MinIndex_j,'String',num2str(MinIndex_j))279 set(handles.MaxIndex_j,'String',num2str(MaxIndex_j))280 259 281 260 … … 336 315 end 337 316 end 317 318 %% set the menu and default choice of civ pairs 319 if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs 320 set(handles.ListPairMode,'Value',1) 321 set(handles.ListPairMode,'String',{'series(Di)'}) 322 elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j 323 set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) 324 if MaxIndex_j <= 10 325 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large 326 end 327 else 328 set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice 329 if strcmp(NomTypeNc,'_1-2_1') 330 set(handles.ListPairMode,'Value',3)% advise 'series(Di)' 331 elseif MaxIndex_j <= 10 332 set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large 333 end 334 end 335 336 %% indicate the min and max indices i and j on the GUI 337 set(handles.MinIndex_i,'String',num2str(MinIndex_i)) 338 set(handles.MaxIndex_i,'String',num2str(MaxIndex_i)) 339 set(handles.MinIndex_j,'String',num2str(MinIndex_j)) 340 set(handles.MaxIndex_j,'String',num2str(MaxIndex_j)) 338 341 339 342 %% set the reference indices from the input file indices … … 968 971 index_pair=0; 969 972 %get all the Time intervals in bursts 973 displ_pair_dt=''; 970 974 for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode 971 975 for numod_b=(numod_a+1):MaxIndex_j … … 981 985 982 986 end 987 if index_pair ~=0 983 988 [tild,indsort]=sort(dt); 984 989 displ_pair=displ_pair(indsort); 985 990 displ_pair_dt=displ_pair_dt(indsort); 991 end 986 992 case 'displacement' 987 993 displ_pair={'Di=Dj=0'}; … … 1497 1503 end 1498 1504 end 1499 set(hObject,'BackgroundColor',[1 0 1])1500 1505 set(handles.ConfigSource,'String','NEW') 1501 1506 set(handles.OK,'BackgroundColor',[1 0 1]) 1507 1502 1508 %------------------------------------------------------------------------ 1503 1509 % --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..) … … 1524 1530 testmask=1; 1525 1531 else % browse for a mask 1526 % filemask=get(hObject,'UserData');%look for previous mask name stored as UserData1527 % if exist(filemask,'file')1528 % filebase=filemask;1529 % end1530 1532 filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image'); 1531 1533 set(hObject,'UserData',filemask);%store for future use -
trunk/src/set_grid.m
r908 r918 24 24 function varargout = set_grid(varargin) 25 25 26 % Last Modified by GUIDE v2.5 01-Mar-2013 22:41:4326 % Last Modified by GUIDE v2.5 26-Jun-2015 08:54:56 27 27 28 28 % Begin initialization code - DO NOT PLOT … … 138 138 UvData=get(huvmat,'UserData'); 139 139 if isfield(UvData.Field, 'CoordUnit')&& strcmp(UvData.Field.CoordUnit,'pixel') 140 plot(grid_pix_A(:,1),grid_pix_A(:,2),'.' )141 else 142 plot(grid_phys(:,1),grid_phys(:,2),'.' )143 end 144 145 %% display grid in second image defi end140 plot(grid_pix_A(:,1),grid_pix_A(:,2),'.','Tag','proj_object') 141 else 142 plot(grid_phys(:,1),grid_phys(:,2),'.','Tag','proj_object') 143 end 144 145 %% display grid in second image defined 146 146 if ~isempty(grid_pix_B) 147 147 hviewfield=view_field(get(handles.imageB,'String')); … … 156 156 end 157 157 158 % --- Executes on button press in clear. 159 function clear_Callback(hObject, eventdata, handles) 160 huvmat=findobj(allchild(0),'tag','uvmat'); 161 if ~isempty(huvmat) 162 hhuvmat=guidata(huvmat); 163 hpoints=findobj(hhuvmat.PlotAxes,'Tag','proj_object'); 164 if ~isempty(hpoints) 165 delete(hpoints) 166 end 167 end 158 168 %------------------------------------------------------------------------ 159 169 % --- Executes on button press in CoordType. … … 184 194 YA=grid_pix_A(:,2); 185 195 unitcolumn=32*ones(size(XA)); 186 Xchar=num2str(XA );196 Xchar=num2str(XA,2); 187 197 blanc=char(unitcolumn); 188 Ychar=num2str(YA );198 Ychar=num2str(YA,2); 189 199 tete=['1 ' num2str(nbpointsA(1))]; 190 200 txt=[Xchar blanc Ychar]; … … 359 369 % Hints: get(hObject,'String') returns contents of ImageA as text 360 370 % str2double(get(hObject,'String')) returns contents of ImageA as a double 371 372 373 374
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