Index: trunk/src/cluster_command.m
===================================================================
--- trunk/src/cluster_command.m (revision 1170)
+++ trunk/src/cluster_command.m (revision 1171)
@@ -33,5 +33,6 @@
corestring='cpu=1/core=4'; %increases the allowed memory in case of single core job
else
- corestring=['/core=' num2str(NbCore)];
+ % corestring=['/core=' num2str(NbCore)];
+ corestring=['{cluster=''calcul8''}/core=' num2str(NbCore)];
end
cmd=['oarsub -n UVmat_' ActionFullName ' '...
Index: trunk/src/series.m
===================================================================
--- trunk/src/series.m (revision 1170)
+++ trunk/src/series.m (revision 1171)
@@ -138,13 +138,17 @@
if ~exist(xmlfile,'file')
[success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
+ if success==0
+ disp(message)
+ return
+ end
end
if exist(xmlfile,'file')
- SeriesData=xml2struct(xmlfile);
+ SeriesData=xml2struct(xmlfile);% read the xml file containing parameters for series computations
if ~(isfield(SeriesData,'ClusterParam')&& isfield(SeriesData.ClusterParam,'LaunchCmdFcn'))
- [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
+ [success,message]=copyfile(xmlfile,fullfile(path_series,'series.xml~'));% backup the file series.xml, not correctly documented
delete(xmlfile);
- [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
- end
- SeriesData=xml2struct(xmlfile);
+ [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);% use the defualt series.xml
+ end
+ SeriesData=xml2struct(xmlfile);% read again the xml file containing parameters for series computations
end
@@ -160,18 +164,19 @@
ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
-if isfield(SeriesData.ClusterParam.ExistenceTest,'Text')
- oarcommand=SeriesData.ClusterParam.ExistenceTest.Text;
+if isfield(SeriesData.ClusterParam, 'ExistenceTest')
+ oarcommand=SeriesData.ClusterParam.ExistenceTest;
+ [s,w]=system(oarcommand); % look for cluster system presence
+ if isequal(s,0)% cluster detected
+ RunModeList=[RunModeList;{'cluster'}];
+ set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
+ set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
+ set(handles.num_CPUTime,'String','')% default CPU time undefined
+ set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
+ end
+ set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
else
- oarcommand=SeriesData.ClusterParam.ExistenceTest;
-end
-[s,w]=system(oarcommand); % look for cluster system presence
-if isequal(s,0)
- RunModeList=[RunModeList;{'cluster'}];
- set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
- set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
- set(handles.num_CPUTime,'String','')% default CPU time undefined
- set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
-end
-set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
+ disp('no cluster availability test in series.xml')
+end
+
%% list of builtin transform functions in the menu TransformName
@@ -1438,24 +1443,8 @@
if strcmp(RunMode,'local')
current_dir=pwd; % current working dir
-cd(ActionPath)
-h_fun=str2func(ActionName);% create the function handle for the function ActionName
-cd(current_dir)
- % if ~isequal(ActionPath,path_series)
- %
- % %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
- % if ~exist(ActionPath,'dir')
- % errormsg=['The prescribed function path ' ActionPath ' does not exist'];
- % return
- % end
- % spath=fileparts(which(ActionName));
- % if ~strcmp(spath,ActionPath)
- % addpath(ActionPath)% add the prescribed path if not the current one
- % end
- % end
- % eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
- % if ~isequal(ActionPath,path_series)
- % rmpath(ActionPath)% add the prescribed path if not the current one
- % end
- end
+ cd(ActionPath)
+ h_fun=str2func(ActionName);% create the function handle for the function ActionName
+ cd(current_dir)
+end
%% Get parameters from series.xml
@@ -1533,30 +1522,4 @@
% NbCore is the number of computer processors used
% NbProcess is the number of independent processes in which the required calculation is split.
-% switch RunMode
-% case {'local','background'}
-% NbCore=1; % no need to split the calculation
-% case 'cluster'
-% %proposed number of cores to reserve in the cluster
-% NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised;
-% NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax);
-% if NbCoreMax~=1
-% if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
-% warning_string=', preferably use .sh option to save Matlab licences';
-% else
-% warning_string=')';
-% end
-% answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
-% if isempty(answer)
-% errormsg='Action launch interrupted by user';
-% return
-% end
-% NbCore=str2double(answer);
-% if NbCore > NbCoreMax
-% NbCore=NbCoreMax;
-% end
-% else
-% NbCore=1;
-% end
-% end
if ~isfield(Param.IndexRange,'NbSlice')
Param.IndexRange.NbSlice=[];
@@ -1586,42 +1549,28 @@
for iexp=1:numel(ListExp)
if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
- %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
-% NbExp=NbExp+1;
-% ExpIndex{NbExp}=iexp;
-% for idevice=1:numel(ListDevices)
-% lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
-% regexprep(ListDevices{idevice},'^\+/',''));
-% lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
-% regexprep(ListDevices{idevice},'^\+/',''));
-% ldir=regexprep(ListDataSeries{idevice},'^\+/','');
-% ListPath{idevice,NbExp}=lpath;
-% ListPathOut{idevice,NbExp}=lpathout;
-% ListSubdir{idevice,NbExp}=ldir;
-% end
- %else
- for idevice=1:numel(ListDevices)
- if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
- for isubdir=1:numel(ListDataSeries)
- if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
- lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
- regexprep(ListDevices{idevice},'^\+/',''));
- lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
- regexprep(ListDevices{idevice},'^\+/',''));
- ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
- if exist(fullfile(lpath,ldir),'dir')
- NbExp=NbExp+1;
- ExpIndex(NbExp)=ExpIndices(iexp);
- DeviceIndex(NbExp)=DeviceIndices(idevice);
- ListPath{NbExp}=lpath;
- ListPathOut{NbExp}=lpathout;
- ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
- ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
- ListSubdir{NbExp}=ldir;
- end
+ for idevice=1:numel(ListDevices)
+ if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
+ for isubdir=1:numel(ListDataSeries)
+ if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
+ lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
+ regexprep(ListDevices{idevice},'^\+/',''));
+ lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
+ regexprep(ListDevices{idevice},'^\+/',''));
+ ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
+ if exist(fullfile(lpath,ldir),'dir')
+ NbExp=NbExp+1;
+ ExpIndex(NbExp)=ExpIndices(iexp);
+ DeviceIndex(NbExp)=DeviceIndices(idevice);
+ ListPath{NbExp}=lpath;
+ ListPathOut{NbExp}=lpathout;
+ ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
+ ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
+ ListSubdir{NbExp}=ldir;
end
end
end
end
-% end
+ end
+ % end
end
end
@@ -1829,6 +1778,16 @@
Param.Action.CPUTime=CPUTime;
end
- JobNumberMax=SeriesData.ClusterParam.JobNumberMax;
- JobCPUTimeAdvised=SeriesData.ClusterParam.JobCPUTimeAdvised;
+ if isfield(SeriesData.ClusterParam,'JobNumberMax')
+ JobNumberMax=SeriesData.ClusterParam.JobNumberMax;
+ else
+ disp('ClusterParam.JobNumberMax not documented in series.xml, set to 500 by default')
+ JobNumberMax=500;
+ end
+ if isfield(SeriesData.ClusterParam,'JobCPUTimeAdvised')
+ JobCPUTimeAdvised=SeriesData.ClusterParam.JobCPUTimeAdvised;
+ else
+ disp('ClusterParam.JobCPUTimeAdvised not documented in series.xml, set to 120 minutes by default')
+ JobCPUTimeAdvised=120;
+ end
if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength such that the typical CPU time of a job is JobCPUTimeAdvised.
@@ -1838,8 +1797,18 @@
NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
end
-
+
% %proposed number of cores to reserve in the cluster
- NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised;
- NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
+ if isfield(SeriesData.ClusterParam,'NbCoreAdvised')
+ NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised;
+ else
+ disp('ClusterParam.NbCoreAdvised not documented in series.xml, set to 16 by default')
+ NbCoreAdvised=16;
+ end
+ if isfield(SeriesData.ClusterParam,'NbCoreMax')
+ NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
+ else
+ disp('ClusterParam.NbCoreMax not documented in series.xml, set to 36 by default')
+ NbCoreMax=min(NbProcess,36);
+ end
if NbCoreMax~=1
if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
@@ -1848,6 +1817,6 @@
warning_string=')';
end
- answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
- if isempty(answer)
+ answer=msgbox_uvmat('INPUT_TXT',['Number of cores (limited to ' num2str(NbCoreMax) warning_string],num2str(NbCoreAdvised));
+ if isempty(answer)||strcmp(answer,'Cancel')
errormsg='Action launch interrupted by user';
return
@@ -2106,5 +2075,10 @@
end
CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
+ if isfield(SeriesData.ClusterParam,'LaunchCmdFcn')&& exist(SeriesData.ClusterParam.LaunchCmdFcn,'file')
LaunchCmdFcn=SeriesData.ClusterParam.LaunchCmdFcn;% command obtained from the function
+ else
+ disp('no ClusterParam.LaunchCmdFcn defined in series.xml')
+ return
+ end
oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
[status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
Index: trunk/src/series.xml.default
===================================================================
--- trunk/src/series.xml.default (revision 1170)
+++ trunk/src/series.xml.default (revision 1171)
@@ -3,5 +3,5 @@
quota -s -g -A
- oarstat
+ oarstat
16
36
Index: trunk/src/series/civ_input.m
===================================================================
--- trunk/src/series/civ_input.m (revision 1170)
+++ trunk/src/series/civ_input.m (revision 1171)
@@ -1564,8 +1564,8 @@
r=regexp(str_civ,'^\D(?[i|j])=( -| )(?\d+)\|(?\d+)','names');
if ~isempty(r)
- if strmp(r.ind,'i')
+ if strcmp(r.ind,'i')
i1=i1-str2num(r.num1);
i2=i2 +str2num(r.num2);
- elseif strmp(r.ind,'j')
+ elseif strcmp(r.ind,'j')
j1=j1-str2num(r.num1);
j2=j2 +str2num(r.num2);