Changeset 1114

Timestamp:

Mar 18, 2022, 12:31:32 PM (2 years ago)

Author:

sommeria

Message:

a few bugs repaired

Location:

trunk/src

Files:

• cluster_command.m (modified) (1 diff)
• proj_field.m (modified) (1 diff)
• series.m (modified) (9 diffs)
• series/merge_proj.m (modified) (1 diff)
• series/sliding_average.m (modified) (3 diffs)
• series/time_series.m (modified) (1 diff)

trunk/src/cluster_command.m

@@ -29 +29 @@
 WallTimeOneProcess=min(4*CPUTimeProcess+10,WallTimeTotal*60/2); % estimated max time of an individual process, used for checkpoint: 
                                                                 %if less than this time remains before walltime, the job is stopped and a new one can be launched ( by the option 'idempotent')
-cmd=['oarsub -n UVmat_' ActionFullName ' '...
+
+      if NbCore==1
+          corestring='cpu=1/core=4'; %increases the allowed memory in case of single core job
+      else
+          corestring=['/core=' num2str(NbCore)]; 
+      end
+                                                                cmd=['oarsub -n UVmat_' ActionFullName ' '...
             '-t idempotent --checkpoint ' num2str(WallTimeOneProcess*60) ' '...
-            '-l "/core=' num2str(NbCore)...
-            bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster
+            '-l "' corestring bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster
             ',walltime=' datestr(WallTimeTotal/24,13) '" '...
             '-E ' filename_errors ' '...

trunk/src/proj_field.m

@@ -237 +237 @@
                     ProjData.(VarName)(ipoint,1)=mean(Var);
                     if isequal(ObjectData.ProjMode,'interp_lin')
-                         ProjData.(VarName)(ipoint,1)=griddata_uvmat(coord_x(indsel),coord_y(indsel),Var,Xpoint(1),Xpoint(2));
+                         ProjData.(VarName)(ipoint,1)=griddata(coord_x(indsel),coord_y(indsel),Var,Xpoint(1),Xpoint(2));
                     end
                end

trunk/src/series.m

@@ -1583 +1583 @@
 % 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.SeriesParam.ClusterParam.NbCoreAdvised;
-        NbCoreMax=SeriesData.SeriesParam.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
+% 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.SeriesParam.ClusterParam.NbCoreAdvised;
+%         NbCoreMax=min(NbProcess,SeriesData.SeriesParam.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=[];
@@ -1866 +1866 @@
     end
     nbfield_j=numel(ref_j); % number of j indices
-    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
+    BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess
     NbProcess=1;
+    NbCore=1;
     switch RunMode
         case 'cluster'
-            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime))
+            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(Param.Action.CPUTime))
                 CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
             else
@@ -1887 +1888 @@
                 NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
             end
-            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
+
+            %         %proposed number of cores to reserve in the cluster
+            NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
+            NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
+            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
+            end
         otherwise
             if ~isempty(Param.IndexRange.NbSlice)
@@ -1893 +1913 @@
             end
     end
-    
+
     %% record nbre of output files and starting time for computation for status
     StatusData=get(handles.status,'UserData');
@@ -1908 +1928 @@
     StatusData.TimeStart=now;
     set(handles.status,'UserData',StatusData)
-    
+
     %% case of a function in Python
     if strcmp(ActionExt, '.py (in dev.)')
@@ -2468 +2488 @@
 current_dir=pwd; % current working dir
 cd(ActionPath)
-h_fun=str2func(ActionName);
+h_fun=str2func(ActionName);% create the function handle for the function ActionName
 cd(current_dir)
 
@@ -3358 +3378 @@
 TransformPathList=get(handles.TransformName,'UserData');
 nb_builtin_transform=4;
-if isequal(TransformName,'more...');     
+
+%% browse transform functions with the input menu option more...
+if isequal(TransformName,'more...')% browse transform functions     
     FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
     if isempty(FileName)
@@ -3393 +3415 @@
 end
 
-%display the current function path
+%% display the current function path
 set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
 set(handles.TransformName,'UserData',TransformPathList);
@@ -3413 +3435 @@
         ParamIn.TransformInput=SeriesData.TransformInput;
     end
-    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
-    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
-    %DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
+    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters
     if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
         SeriesData.TransformInput=DataOut.TransformInput;

trunk/src/series/merge_proj.m

@@ -113 +113 @@
 RootFile=Param.InputTable(:,3);
 SubDir=Param.InputTable(:,2);
-NomType=Param.InputTable(:,4);
+% NomType=Param.InputTable(:,4);
 FileExt=Param.InputTable(:,5);
 

trunk/src/series/sliding_average.m

@@ -16 +16 @@
 % Param contains the elements:(use the menu bar command 'export/GUI config' in series to 
 % see the current structure Param)
-%    .InputTable: cell of input file names, (several lines for multiple input)
+%    .InputTable: cell of input file names, (several5.804 lines for multiple input)
 %                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
 %    .OutputSubDir: name of the subdirectory for data outputs
@@ -179 +179 @@
 if isfield(Param,'InputFields')
     InputFields{1}=Param.InputFields;
-end
+end5.804
 
 nbfiles=0;
 nbmissing=0;
 
-%% initialisation
+%% initialisation manip Coriolis
 char_index=regexp(SubDir{1},'waves_L1_');
 switch(SubDir{1}(char_index+9))
@@ -242 +242 @@
         break
     end
-    [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
+    [Field,tild,~] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
     
     %%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%

trunk/src/series/time_series.m

@@ -214 +214 @@
 
 %% coordinate transform or other user defined transform
-transform_fct=[];%default
+transform_fct='';%default fct handle
 if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
-    %addpath(Param.FieldTransform.TransformPath)
+    currentdir=pwd;
+    cd(Param.FieldTransform.TransformPath)
     transform_fct=str2func(Param.FieldTransform.TransformName);
-    %rmpath(Param.FieldTransform.TransformPath)
+    cd (currentdir)
     if isfield(Param,'TransformInput')
-        XmlData{1}.TransformInput=Param.TransformInput;
-    end
+        for iview=1:NbView
+            XmlData{iview}.TransformInput=Param.TransformInput;
+        end
+    end       
 end