Index: /issm/trunk/src/m/utils/Nightly/runme.m
===================================================================
--- /issm/trunk/src/m/utils/Nightly/runme.m	(revision 2125)
+++ /issm/trunk/src/m/utils/Nightly/runme.m	(revision 2125)
@@ -0,0 +1,187 @@
+function varargout=runme(varargin)
+%RUNME - test deck for ISSM nightly runs
+%
+%   Usage:
+%      varargout=runme(varargin);
+%
+%   Examples:
+%      runme;
+%      runme({'ice'});
+%      runme({'ice','cielo_serial'},{'diagnostic'});
+%      md=runme({'cielo_parallel'});
+%
+%   See Also: UPDATEARCHIVE
+
+% This file can be run to check that the current version of issm is giving 
+% coherent results. This test deals with an icesheet without icefront for a 2d model. The geometry 
+% is square. Just run this file in Matlab, with a properly setup ISSM code. 
+% The results of this test will indicate if there is a difference between current computations 
+% and archived results.
+
+% Errors  between archived results and the current version will get flagged if they are not within 
+% a certain tolerance. The current tolerance is 10^-12. If you have good reasons to believe this 
+% tolerance should be lowered (for example, if you are running single precision compilers?), feel 
+% free to tweak the tolerance variable.
+
+%recover options
+options=recover_options(varargin{:});
+
+%check arguments
+if nargout>1
+	help runme
+	error('runme error message: bad usage');
+end
+
+%warning if a runme already exists:
+if exist('./runme.m')
+	disp('this is the nighlty run runme, located in src/m/utils/Nightly/runme.m')
+	disp('Another local runme exist but is not executed')
+end
+
+%read configuration
+configuration;
+
+%packages and analysis_types to be tested
+if nargin==2,
+	solutions=varargin{2};
+end
+
+if nargin,
+	packages=varargin{1};
+end
+
+%go through the sequences requested.
+for i=1:size(sequences,1),
+	sequence=sequences{i};
+
+	%recover what is being requested.
+	analysis_type=sequence{1};
+	sub_analysis_type=sequence{2};
+	qmu=sequence{3};
+	control=sequence{4};
+	control_fit=sequence{5};
+	parallel=sequence{6};
+
+	%CHECK analysis_type
+	analysis_type_arg=find_option(options,'analysis_type');
+	if ~isempty(analysis_type_arg),
+		if ~ismember(analysis_type,analysis_type_arg)
+			continue
+		end
+	end
+
+	%CHECK sub_analysis_type
+	sub_analysis_type_arg=find_option(options,'sub_analysis_type');
+	if ~isempty(sub_analysis_type_arg),
+		if ~ismember(sub_analysis_type,sub_analysis_type_arg)
+			continue
+		end
+	end
+
+	%CHECK parallel
+	parallel_arg=find_option(options,'parallel');
+	if ~isempty(parallel_arg),
+		if parallel~=parallel_arg,
+			continue
+		end
+	end
+
+	%initialize model, using presolve if need be, or just the piece of generic code below.
+	md=model;
+	if ~rifts,
+		md=mesh(md,domainname,resolution);
+	else
+		md=mesh(md,domainname,riftoutline,resolution);
+		md=meshprocessrifts(md);
+	end
+	md=geography(md,iceshelfname,icesheetname);
+	md=parameterize(md,parametername);
+	md=extrude(md,numlayers,extrusionexponent);
+	eval(['md=setelementstype(md,' elementstype ');']);
+
+	if parallel, 
+		%this run will be done in parallel
+		md.cluster=oshostname;
+		%check and modify number of cpus if necessary
+		np=feature('numCores');
+		if np<md.np;
+			disp(['warning: changing number of cpus to ' num2str(np) ]);
+			md.np=np;
+		end
+		runtype='parallel';
+	else
+		runtype='serial';
+	end
+
+	%some solution checks;
+	if (  (strcmpi(analysis_type,'thermal') & strcmpi(sub_analysis_type,'steady')) | ...
+			(strcmpi(analysis_type,'steadystate'))...
+		)
+		md.dt=0;
+	end
+
+	if control,
+		md.control_analysis=1;
+		if strcmpi(control_fit,'absolute'),
+			md.fit(:)=0;
+		elseif strcmpi(control_fit,'relative'),
+			md.fit(:)=1;
+		elseif strcmpi(control_fit,'logarithmic'),
+			md.fit(:)=2;
+		else
+			error(['runme error message: for control solution, ' control_fit ' fit is not supported!']);
+		end
+	end
+	
+	%try to run the test
+	try,
+
+		%presolve
+		if exist('./testpresolve.m','file')==2,
+			testpresolve;
+		end
+
+		%solve
+		md=solve(md,'analysis_type',analysis_type,'sub_analysis_type',sub_analysis_type);
+
+		%postsolve
+		if exist('./testpostsolve.m','file')==2,
+			testpostsolve;
+		end
+
+		%compute fields to be checked
+		fields=testsgetfields2(md,sequence);
+
+		%load archive
+		eval(['load Archive_'  analysis_type '_' sub_analysis_type '_' runtype ]);
+
+		for k=1:length(fields),
+
+			%Get field and tolerance
+			field=fields{k};
+			tolerance=testsgettolerance2(md,sequence);
+
+			%compare to archive
+			eval(['Archive=Archive_'  analysis_type '_' sub_analysis_type '_' runtype '_field' num2str(k) ';']);
+			eval(['error_diff=full(max(abs(Archive-md.results.' field '))/(max(abs(Archive))+eps));']);
+
+			%disp test result
+			if (error_diff>tolerance);
+				disp(sprintf(['\nERROR   difference: %-7.2g > %7.2g test: %-25s solution: %-16s type: %-9s field: ' field  '.\n\n'],error_diff,tolerance,testname,[analysis_type '_' sub_analysis_type],runtype));
+			else
+				disp(sprintf(['\nSUCCESS difference: %-7.2g < %7.2g test: %-25s solution: %-16s type: %-9s field: ' field  '.\n\n'],error_diff,tolerance,testname,[analysis_type '_' sub_analysis_type],runtype));
+			end
+		end
+
+	catch me,
+
+		%something went wrong, print failure message:
+		message=getReport(me)
+		disp(sprintf(['\n\nFAILURE difference: %-16s test: %-25s solution: %-16s type: %-9s field: ' field  '.\n\n'],'N/A',testname,[analysis_type '_' sub_analysis_type],runtype));
+	end
+end
+
+%output model md if requested
+if nargout==1, 
+	varargout{1}=md; 
+end
Index: /issm/trunk/src/m/utils/Nightly/updatearchive.m
===================================================================
--- /issm/trunk/src/m/utils/Nightly/updatearchive.m	(revision 2125)
+++ /issm/trunk/src/m/utils/Nightly/updatearchive.m	(revision 2125)
@@ -0,0 +1,171 @@
+function varargout=updatearchive(varargin)
+%RUNME - test deck for ISSM nightly runs
+%
+%   Usage:
+%      varargout=updatearchive(varargin);
+%
+%   Examples:
+%      updatearchive;
+%      updatearchive({'ice'});
+%      updatearchive({'ice','cielo_serial'},{'diagnostic'});
+%      md=updatearchive({'cielo_parallel'});
+%
+%   See Also: UPDATEARCHIVE
+
+% This file can be run to check that the current version of issm is giving 
+% coherent results. This test deals with an icesheet without icefront for a 2d model. The geometry 
+% is square. Just run this file in Matlab, with a properly setup ISSM code. 
+% The results of this test will indicate if there is a difference between current computations 
+% and archived results.
+
+% Errors  between archived results and the current version will get flagged if they are not within 
+% a certain tolerance. The current tolerance is 10^-12. If you have good reasons to believe this 
+% tolerance should be lowered (for example, if you are running single precision compilers?), feel 
+% free to tweak the tolerance variable.
+
+%check arguments
+if (nargin>2 | nargout>1)
+	help updatearchive
+	error('updatearchive error message: bad usage');
+end
+
+%warning if a updatearchive already exists:
+if exist('./updatearchive.m')
+	disp('this is the nighlty run updatearchive, located in src/m/utils/Nightly/updatearchive.m')
+	disp('Another local updatearchive exist but is not executed')
+end
+
+%recover options
+options=recover_options(varargin{:});
+
+%read configuration
+configuration;
+
+%packages and analysis_types to be tested
+if nargin==2,
+	solutions=varargin{2};
+end
+
+if nargin,
+	packages=varargin{1};
+end
+
+%go through the sequences requested.
+for i=1:size(sequences,1),
+	sequence=sequences{i};
+
+	%recover what is being requested.
+	analysis_type=sequence{1};
+	sub_analysis_type=sequence{2};
+	qmu=sequence{3};
+	control=sequence{4};
+	control_fit=sequence{5};
+	parallel=sequence{6};
+
+	%CHECK analysis_type
+	analysis_type_arg=find_option(options,'analysis_type');
+	if ~isempty(analysis_type_arg),
+		if ~ismember(analysis_type,analysis_type_arg)
+			continue
+		end
+	end
+
+	%CHECK sub_analysis_type
+	sub_analysis_type_arg=find_option(options,'sub_analysis_type');
+	if ~isempty(sub_analysis_type_arg),
+		if ~ismember(sub_analysis_type,sub_analysis_type_arg)
+			continue
+		end
+	end
+
+	%CHECK parallel
+	parallel_arg=find_option(options,'parallel');
+	if ~isempty(parallel_arg),
+		if parallel~=parallel_arg,
+			continue
+		end
+	end
+
+	%initialize model, using presolve if need be, or just the piece of generic code below.
+	md=model;
+	if ~rifts,
+		md=mesh(md,domainname,resolution);
+	else
+		md=mesh(md,domainname,riftoutline,resolution);
+		md=meshprocessrifts(md);
+	end
+	md=geography(md,iceshelfname,icesheetname);
+	md=parameterize(md,parametername);
+	md=extrude(md,numlayers,extrusionexponent);
+	eval(['md=setelementstype(md,' elementstype ');']);
+
+	if parallel, 
+		%this run will be done in parallel
+		md.cluster=oshostname;
+		%check and modify number of cpus if necessary
+		np=feature('numCores');
+		if np<md.np;
+			disp(['warning: changing number of cpus to ' num2str(np) ]);
+			md.np=np;
+		end
+		runtype='parallel';
+	else
+		runtype='serial';
+	end
+
+	%some solution checks;
+	if (  (strcmpi(analysis_type,'thermal') & strcmpi(sub_analysis_type,'steady')) | ...
+			(strcmpi(analysis_type,'steadystate'))...
+		)
+		md.dt=0;
+	end
+
+	if control,
+		md.control_analysis=1;
+		if strcmpi(control_fit,'absolute'),
+			md.fit(:)=0;
+		elseif strcmpi(control_fit,'relative'),
+			md.fit(:)=1;
+		elseif strcmpi(control_fit,'logarithmic'),
+			md.fit(:)=2;
+		else
+			error(['updatearchive error message: for control solution, ' control_fit ' fit is not supported!']);
+		end
+	end
+	
+	%presolve
+	if exist('./testpresolve.m','file')==2,
+		testpresolve;
+	end
+
+	%solve
+	md=solve(md,'analysis_type',analysis_type,'sub_analysis_type',sub_analysis_type);
+
+	%postsolve
+	if exist('./testpostsolve.m','file')==2,
+		testpostsolve;
+	end
+	md=solve(md,'analysis_type',analysis_type,'sub_analysis_type',sub_analysis_type);
+
+	%compute fields to be checked
+	fields=testsgetfields2(md,sequence);
+
+	%save new archive
+	if parallel,
+		runtype='parallel';
+	else
+		runtype='serial';
+	end
+	for k=1:length(fields),
+		field=fields{k};
+		eval(['Archive_'  analysis_type '_' sub_analysis_type '_' runtype '_field' num2str(k) ' = md.results. ' field  ';']);
+	end
+	eval(['save Archive_'  analysis_type '_' sub_analysis_type '_' runtype ' Archive_'  analysis_type '_' sub_analysis_type '_' runtype '_field*']);
+	disp(sprintf(['File Archive_'  analysis_type '_' sub_analysis_type '_' runtype ' saved\n']));
+
+end
+
+%output model md if requested
+if nargout==1, 
+	varargout{1}=md; 
+end