Changeset 9702

Timestamp:

09/08/11 15:48:24 (14 years ago)

Author:

Mathieu Morlighem

Message:

Added autofiff.m class and moved some other fields to settings

Location:

issm/trunk

Files:

• src/c/EnumDefinitions/EnumDefinitions.h (modified) (5 diffs)
• src/c/modules/EnumToStringx/EnumToStringx.cpp (modified) (5 diffs)
• src/c/modules/ModelProcessorx/CreateParameters.cpp (modified) (2 diffs)
• src/c/modules/StringToEnumx/StringToEnumx.cpp (modified) (5 diffs)
• src/c/solutions/issm.cpp (modified) (1 diff)
• src/c/solutions/transient_core.cpp (modified) (1 diff)
• src/m/classes/autofiff.m (added)
• src/m/classes/model/model.m (modified) (4 diffs)
• src/m/classes/settings.m (modified) (2 diffs)
• src/m/enum/AdAnalysisEnum.m (deleted)
• src/m/enum/AdForwardEnum.m (deleted)
• src/m/enum/AdReverseEnum.m (deleted)
• src/m/enum/AutodiffAnalysisEnum.m (added)
• src/m/enum/AutodiffForwardEnum.m (added)
• src/m/enum/AutodiffReverseEnum.m (added)
• src/m/enum/OutputFrequencyEnum.m (deleted)
• src/m/enum/ResultsOnVerticesEnum.m (deleted)
• src/m/enum/SettingsOutputFrequencyEnum.m (added)
• src/m/enum/SettingsResultsOnVerticesEnum.m (added)
• src/m/enum/SettingsWaitonlockEnum.m (added)
• src/m/enum/ThicknessCoeffEnum.m (deleted)
• src/m/enum/WaitonlockEnum.m (deleted)
• src/m/model/ismodelselfconsistent.m (modified) (1 diff)
• src/m/model/loadresultsfromcluster.m (modified) (1 diff)
• src/m/model/loadresultsfromdisk.m (modified) (1 diff)
• src/m/model/solveparallel.m (modified) (1 diff)
• src/m/model/waitonlock.m (modified) (2 diffs)
• src/m/solutions/transient_core.m (modified) (1 diff)
• template (modified) (1 diff)
• test/Miscellaneous/Bump/Bump.par (modified) (1 diff)
• test/Miscellaneous/GJM_test1/SquareShelf.par (modified) (1 diff)
• test/Miscellaneous/connectivity/Square.par (modified) (1 diff)
• test/Par/79North.par (modified) (1 diff)
• test/Par/Pig.par (modified) (1 diff)
• test/Par/RoundSheetShelf.par (modified) (1 diff)
• test/Par/SquareSheetConstrained.par (modified) (1 diff)
• test/Par/SquareSheetShelf.par (modified) (1 diff)
• test/Par/SquareShelf.par (modified) (1 diff)
• test/Par/SquareShelfConstrained.par (modified) (1 diff)

issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h

@@ -35 +35 @@
         SettingsLowmemEnum,
         SettingsIoGatherEnum,
+        SettingsResultsOnVerticesEnum,
+        SettingsOutputFrequencyEnum,
+        SettingsWaitonlockEnum,
         ThermalSpctemperatureEnum,
         ThermalPenaltyThresholdEnum,
@@ -141 +144 @@
         BathymetryEnum,
         SurfaceEnum,
+        AutodiffAnalysisEnum, 
+        AutodiffForwardEnum,
+        AutodiffReverseEnum,
         /*}}}*/
         /*Datasets {{{1*/
@@ -364 +370 @@
         PatchNodesEnum,
         TimeEnum,
-        OutputFrequencyEnum,
         WaterColumnOldEnum,
         /*}}}*/
@@ -472 +477 @@
         WaterfractionEnum,
         WatercolumnEnum,
-        WaitonlockEnum,
         NumberOfResponsesEnum,
         BasalFrictionEnum,
@@ -481 +485 @@
         SpcDynamicEnum,
         NumberOfEdgesEnum,
-        ResultsOnVerticesEnum,
-        /*Automatic Differentiation {{{1*/
-        AdAnalysisEnum, 
-        AdForwardEnum,
-        AdReverseEnum,
-        /*}}}*/
+
         MaximumNumberOfEnums
 };

issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp

@@ -39 +39 @@
                 case SettingsLowmemEnum : return "SettingsLowmem";
                 case SettingsIoGatherEnum : return "SettingsIoGather";
+                case SettingsResultsOnVerticesEnum : return "SettingsResultsOnVertices";
+                case SettingsOutputFrequencyEnum : return "SettingsOutputFrequency";
+                case SettingsWaitonlockEnum : return "SettingsWaitonlock";
                 case ThermalSpctemperatureEnum : return "ThermalSpctemperature";
                 case ThermalPenaltyThresholdEnum : return "ThermalPenaltyThreshold";
@@ -145 +148 @@
                 case BathymetryEnum : return "Bathymetry";
                 case SurfaceEnum : return "Surface";
+                case AutodiffAnalysisEnum : return "AutodiffAnalysis";
+                case AutodiffForwardEnum : return "AutodiffForward";
+                case AutodiffReverseEnum : return "AutodiffReverse";
                 case ConstraintsEnum : return "Constraints";
                 case ElementsEnum : return "Elements";
@@ -327 +333 @@
                 case PatchNodesEnum : return "PatchNodes";
                 case TimeEnum : return "Time";
-                case OutputFrequencyEnum : return "OutputFrequency";
                 case WaterColumnOldEnum : return "WaterColumnOld";
                 case MinVelEnum : return "MinVel";
@@ -416 +421 @@
                 case WaterfractionEnum : return "Waterfraction";
                 case WatercolumnEnum : return "Watercolumn";
-                case WaitonlockEnum : return "Waitonlock";
                 case NumberOfResponsesEnum : return "NumberOfResponses";
                 case BasalFrictionEnum : return "BasalFriction";
@@ -425 +429 @@
                 case SpcDynamicEnum : return "SpcDynamic";
                 case NumberOfEdgesEnum : return "NumberOfEdges";
-                case ResultsOnVerticesEnum : return "ResultsOnVertices";
-                case AdAnalysisEnum : return "AdAnalysis";
-                case AdForwardEnum : return "AdForward";
-                case AdReverseEnum : return "AdReverse";
                 default : return "unknown";
 

issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp

@@ -29 +29 @@
         parameters->AddObject(iomodel->CopyConstantObject(FlowequationIsmacayealpattynEnum));
         parameters->AddObject(iomodel->CopyConstantObject(FlowequationIsstokesEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(OutputFrequencyEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(SettingsOutputFrequencyEnum));
         parameters->AddObject(iomodel->CopyConstantObject(DiagnosticRestolEnum));
         parameters->AddObject(iomodel->CopyConstantObject(DiagnosticReltolEnum));
@@ -59 +59 @@
         parameters->AddObject(iomodel->CopyConstantObject(DiagnosticShelfDampeningEnum));
         parameters->AddObject(iomodel->CopyConstantObject(DiagnosticViscosityOvershootEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(WaitonlockEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(SettingsWaitonlockEnum));
         parameters->AddObject(iomodel->CopyConstantObject(NumberOfElementsEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SettingsIoGatherEnum));

issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp

@@ -37 +37 @@
         else if (strcmp(name,"SettingsLowmem")==0) return SettingsLowmemEnum;
         else if (strcmp(name,"SettingsIoGather")==0) return SettingsIoGatherEnum;
+        else if (strcmp(name,"SettingsResultsOnVertices")==0) return SettingsResultsOnVerticesEnum;
+        else if (strcmp(name,"SettingsOutputFrequency")==0) return SettingsOutputFrequencyEnum;
+        else if (strcmp(name,"SettingsWaitonlock")==0) return SettingsWaitonlockEnum;
         else if (strcmp(name,"ThermalSpctemperature")==0) return ThermalSpctemperatureEnum;
         else if (strcmp(name,"ThermalPenaltyThreshold")==0) return ThermalPenaltyThresholdEnum;
@@ -143 +146 @@
         else if (strcmp(name,"Bathymetry")==0) return BathymetryEnum;
         else if (strcmp(name,"Surface")==0) return SurfaceEnum;
+        else if (strcmp(name,"AutodiffAnalysis")==0) return AutodiffAnalysisEnum;
+        else if (strcmp(name,"AutodiffForward")==0) return AutodiffForwardEnum;
+        else if (strcmp(name,"AutodiffReverse")==0) return AutodiffReverseEnum;
         else if (strcmp(name,"Constraints")==0) return ConstraintsEnum;
         else if (strcmp(name,"Elements")==0) return ElementsEnum;
@@ -325 +331 @@
         else if (strcmp(name,"PatchNodes")==0) return PatchNodesEnum;
         else if (strcmp(name,"Time")==0) return TimeEnum;
-        else if (strcmp(name,"OutputFrequency")==0) return OutputFrequencyEnum;
         else if (strcmp(name,"WaterColumnOld")==0) return WaterColumnOldEnum;
         else if (strcmp(name,"MinVel")==0) return MinVelEnum;
@@ -414 +419 @@
         else if (strcmp(name,"Waterfraction")==0) return WaterfractionEnum;
         else if (strcmp(name,"Watercolumn")==0) return WatercolumnEnum;
-        else if (strcmp(name,"Waitonlock")==0) return WaitonlockEnum;
         else if (strcmp(name,"NumberOfResponses")==0) return NumberOfResponsesEnum;
         else if (strcmp(name,"BasalFriction")==0) return BasalFrictionEnum;
@@ -423 +427 @@
         else if (strcmp(name,"SpcDynamic")==0) return SpcDynamicEnum;
         else if (strcmp(name,"NumberOfEdges")==0) return NumberOfEdgesEnum;
-        else if (strcmp(name,"ResultsOnVertices")==0) return ResultsOnVerticesEnum;
-        else if (strcmp(name,"AdAnalysis")==0) return AdAnalysisEnum;
-        else if (strcmp(name,"AdForward")==0) return AdForwardEnum;
-        else if (strcmp(name,"AdReverse")==0) return AdReverseEnum;
         else _error_("Enum %s not found",name);
 

issm/trunk/src/c/solutions/issm.cpp

@@ -86 +86 @@
 
         /*get parameters: */
-        femmodel->parameters->FindParam(&waitonlock,WaitonlockEnum);
+        femmodel->parameters->FindParam(&waitonlock,SettingsWaitonlockEnum);
         femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum);
         femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum);

issm/trunk/src/c/solutions/transient_core.cpp

@@ -36 +36 @@
         femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum);
         femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum);
-        femmodel->parameters->FindParam(&output_frequency,OutputFrequencyEnum);
+        femmodel->parameters->FindParam(&output_frequency,SettingsOutputFrequencyEnum);
         femmodel->parameters->FindParam(&time_adapt,TimesteppingTimeAdaptEnum);
         femmodel->parameters->FindParam(&groundingline_migration,GroundinglineMigrationEnum);

issm/trunk/src/m/classes/model/model.m

@@ -82 +82 @@
                  nodeonbed         = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1);
                  nodeonsurface     = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1);
-                 minh              = modelfield('default',0,'marshall',false);
 
                  %Extraction
@@ -93 +92 @@
                  %Statics parameters
                  connectivity             = modelfield('default',0,'marshall',true,'format','Integer');
-
-
-                 %Results fields
-                 output_frequency               = modelfield('default',0,'marshall',true,'format','Integer');
-                 results_on_vertices            = modelfield('default',0,'marshall',true,'format','Boolean');
-
-                 %Parallelisation
-                 outlog        = modelfield('default','','marshall',false);
-                 errlog        = modelfield('default','','marshall',false);
-                 waitonlock    = modelfield('default',0,'marshall',true,'format','Boolean');
-
-                 %ad: automatic differentiation
-                 ad_analysis = modelfield('default',false,'marshall',true,'format','Boolean');
-                 ad_forward = modelfield('default',true,'marshall',true,'format','Boolean');
-                 ad_reverse = modelfield('default',false,'marshall',true,'format','Boolean');
                  %}}}
          end
@@ -477 +461 @@
                          md.initialization   = initialization;
                          md.geometry         = geometry;
-
-                         %Solver parameters
+                         md.verbose          = verbose('solution',true,'qmu',true,'control',true);
 
                          %the connectivity is the avergaded number of nodes linked to a
@@ -486 +469 @@
                          %trunk/test/Miscellaneous/runme.m
                          md.connectivity=25;
-
-
-                         %parameter used to print temporary results (convergence criterion,
-                         %current step,...)
-                         md.verbose=verbose('solution',true,'qmu',true,'control',true);
-
-                         %minimum thickness to avoid stiffness singularity, used in
-                         %the parameter file
-                         md.minh=1;
-
-                         %How often to save results, default is 1 so save every step
-                         md.output_frequency=1;
-
-                         %this option can be activated to load automatically the results
-                         %onto the model after a parallel run by waiting for the lock file
-                         %N minutes that is generated once the solution has converged
-                         %0 to desactivate
-                         md.waitonlock=Inf;
                  end
                  %}}}
-                 function result = subsref(md,index) % {{{1
-
-                         if length(index)==1,
-                                 index1=index(1);
-                                 if(strcmp(index1.subs,'mesh')), displaymesh(md);return; end
-                                 if(strcmp(index1.subs,'bc')), displaybc(md);return; end
-                                 if(strcmp(index1.subs,'mat')), displaymaterials(md);return; end
-                                 if(strcmp(index1.subs,'par')), displayparameters(md);return; end
-                                 if(strcmp(index1.subs,'res')), displayresults(md);return; end
-                                 if(strcmp(index1.subs,'parallel')), displayparallel(md);return; end
-                         end
-
-                         %return built in value
-                         result=builtin('subsref',md,index);
-                 end %}}}
          end
  end

issm/trunk/src/m/classes/settings.m

@@ -6 +6 @@
 classdef settings
         properties (SetAccess=public) 
-                io_gather = modelfield('default',0,'marshall',true,'format','Boolean');
-                lowmem    = modelfield('default',0,'marshall',true,'format','Boolean');
+                io_gather           = modelfield('default',0,'marshall',true,'format','Boolean');
+                lowmem              = modelfield('default',0,'marshall',true,'format','Boolean');
+                results_on_vertices = modelfield('default',0,'marshall',true,'format','Boolean');
+                output_frequency    = modelfield('default',0,'marshall',true,'format','Boolean');
+                waitonlock          = modelfield('default',0,'marshall',true,'format','Boolean');
         end
         methods
@@ -34 +37 @@
                         end
 
-                        %lowmem??
+                        %are we short in memory ? (0 faster but requires more memory)
                         obj.lowmem=0;
 
                         %i/o:
                         obj.io_gather=1;
+
+                        %results frequency by default every step
+                        obj.output_frequency=1;
+
+                        %this option can be activated to load automatically the results
+                        %onto the model after a parallel run by waiting for the lock file
+                        %N minutes that is generated once the solution has converged
+                        %0 to desactivate
+                        md.waitonlock=Inf;
                 end % }}}
         end

issm/trunk/src/m/model/ismodelselfconsistent.m

@@ -284 +284 @@
 if strcmpi(md.private.solution,'qmu'),
         if ~strcmpi(md.cluster.name,'none'),
-                if md.waitonlock==0,
+                if md.settings.waitonlock==0,
                         message(['model is not correctly configured: waitonlock should be activated when running qmu in parallel mode!']);
                 end

issm/trunk/src/m/model/loadresultsfromcluster.m

@@ -14 +14 @@
 %Download outputs from the cluster
 cluster.Download(md);
-
-%read log files onto  fields
-if exist([md.miscellaneous.name '.errlog'],'file'),
-        md.errlog=char(textread([md.miscellaneous.name '.errlog'],'%s','delimiter','\n'));
-else
-        md.errlog='';
-end
-
-if exist([md.miscellaneous.name '.outlog'],'file'),
-        md.outlog=char(textread([md.miscellaneous.name '.outlog'],'%s','delimiter','\n'));
-else
-        md.outlog='';
-end
-
-if ~isempty(md.errlog),
-        disp(['loadresultsfromcluster info message: error during solution. Check your errlog and outlog model fields']);
-end
 
 %If we are here, no errors in the solution sequence, call loadresultsfromdisk.

issm/trunk/src/m/model/loadresultsfromdisk.m

@@ -25 +25 @@
         md.private.solution=structure(1).SolutionType;
 
+        %read log files onto  fields
+        if exist([md.miscellaneous.name '.errlog'],'file'),
+                md.results.(structure(1).SolutionType).errlog=char(textread([md.miscellaneous.name '.errlog'],'%s','delimiter','\n'));
+        else
+                md.results.(structure(1).SolutionType).errlog='';
+        end
+
+        if exist([md.miscellaneous.name '.outlog'],'file'),
+                md.results.(structure(1).SolutionType).outlog=char(textread([md.miscellaneous.name '.outlog'],'%s','delimiter','\n'));
+        else
+                md.iresults.(structure(1).SolutionType).outlog='';
+        end
+
+        if ~isempty(md.results.(structure(1).SolutionType).errlog),
+                disp(['loadresultsfromcluster info message: error during solution. Check your errlog and outlog model fields']);
+        end
+
+
 %post processes qmu results if necessary
 else

issm/trunk/src/m/model/solveparallel.m

@@ -25 +25 @@
 
                 %Do we return, or just wait for results?
-                if (md.waitonlock>0 &  ~strcmpi(options.batch,'yes')),
+                if (md.settings.waitonlock>0 &  ~strcmpi(options.batch,'yes')),
                         %we wait for the done file
                         islock=waitonlock(md);

issm/trunk/src/m/model/waitonlock.m

@@ -13 +13 @@
 login=md.cluster.login;
 port=md.cluster.port;
-timelimit=md.waitonlock;
+timelimit=md.settings.waitonlock;
 filename=[executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.lock'];
 
@@ -49 +49 @@
         %build output
         if (time>timelimit),
-                disp('Time limit exceeded. Increase md.waitonlock');
+                disp('Time limit exceeded. Increase md.settings.waitonlock');
                 disp('The results must be loaded manually with md=loadresultsfromcluster(md).');
                 error(['waitonlock error message: time limit exceeded']);

issm/trunk/src/m/solutions/transient_core.m

@@ -12 +12 @@
         control_analysis=femmodel.parameters.InversionIscontrol;
         solution_type=femmodel.parameters.SolutionType;
-        output_frequency=femmodel.parameters.OutputFrequency;
+        output_frequency=femmodel.parameters.SettingsOutputFrequency;
         time_adapt=femmodel.parameters.TimesteppingTimeAdapt;
         isdiagnostic=femmodel.parameters.TransientIsdiagnostic;

issm/trunk/template

@@ -49 +49 @@
           -> already exists
 }}}
-results{{{
-        results_on_vertices
-          output_frequency
-          outlog
-          errlog
-          + all model results ??? (DiagnosticSolution and others?)
-}}}

issm/trunk/test/Miscellaneous/Bump/Bump.par

@@ -32 +32 @@
 
 %Parallel options
-md.waitonlock=1;
+md.settings.waitonlock=1;
 md.connectivity=100;

issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par

@@ -28 +28 @@
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.verbose=verbose(0);
 md.eps_res=0.10;

issm/trunk/test/Miscellaneous/connectivity/Square.par

@@ -36 +36 @@
 md.np=8;
 md.time=50;
-md.waitonlock=1;
+md.settings.waitonlock=1;
 md.debug=1;

issm/trunk/test/Par/79North.par

@@ -34 +34 @@
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;

issm/trunk/test/Par/Pig.par

@@ -31 +31 @@
 md.prognostic.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.timestepping.time_step=1;
 md.timestepping.final_time=2;

issm/trunk/test/Par/RoundSheetShelf.par

@@ -61 +61 @@
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.diagnostic.restol=0.05;
 md.diagnostic.reltol=0.05;

issm/trunk/test/Par/SquareSheetConstrained.par

@@ -35 +35 @@
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.diagnostic.restol=0.05;
 md.steadystate.reltol=0.05;

issm/trunk/test/Par/SquareSheetShelf.par

@@ -42 +42 @@
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.diagnostic.restol=0.05;
 md.steadystate.reltol=0.05;

issm/trunk/test/Par/SquareShelf.par

@@ -34 +34 @@
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.verbose=verbose(0);
 md.diagnostic.restol=0.10;

issm/trunk/test/Par/SquareShelfConstrained.par

@@ -39 +39 @@
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
-md.waitonlock=30;
+md.settings.waitonlock=30;
 md.diagnostic.restol=0.05;
 md.diagnostic.reltol=0.05;