Index: /issm/trunk/src/m/classes/clusters/murdo.m
===================================================================
--- /issm/trunk/src/m/classes/clusters/murdo.m	(revision 7303)
+++ /issm/trunk/src/m/classes/clusters/murdo.m	(revision 7303)
@@ -0,0 +1,152 @@
+%MURDO class definition
+%
+%   Usage:
+%      cluster=murdo();
+%      cluster=murdo('np',3);
+%      cluster=murdo('np',3,'login','username');
+
+classdef murdo
+    properties (SetAccess=public) 
+		 % {{{1
+		 name='murdo';
+		 login='larour';
+		 np=24;
+		 port=0;
+		 codepath=[issmtier() '/bin'];
+		 executionpath=[issmdir() '/execution'];
+		 valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind'];
+		 valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
+		 valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp'];
+
+		 %}}}
+	 end
+	 methods
+		 function cluster=murdo(varargin) % {{{1
+		 
+			 %initialize cluster using user settings if provided
+			 if (exist('murdo_settings')==2), murdo_settings; end
+
+			 %use provided options to change fields
+			 options=pairoptions(varargin{:});
+			 for i=1:size(options.list,1),
+				 fieldname=options.list{i,1};
+				 fieldvalue=options.list{i,2};
+				 if ismember(fieldname,properties(murdo)),
+					 cluster.(fieldname)=fieldvalue;
+				 else
+					 disp(['''' fieldname ''' is not a property of cluster murdo']);
+				 end
+			 end
+		 end
+		 %}}}
+		 function disp(cluster) % {{{1
+			 %  display the object
+			 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
+			 disp(sprintf('    name: %s',cluster.name));
+			 disp(sprintf('    login: %s',cluster.login));
+			 disp(sprintf('    np: %i',cluster.np));
+			 disp(sprintf('    port: %i',cluster.port));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    valgrind: %s',cluster.valgrind));
+			 disp(sprintf('    valgrindlib: %s',cluster.valgrindlib));
+			 disp(sprintf('    valgrindsup: %s',cluster.valgrindsup));
+		 end
+		 %}}}
+		 function IsConsistent(cluster) % {{{1
+			 if cluster.np>24,
+				 error('IsConsistent error message: number of processors should be less than 24!');
+			 end
+			 if isnan(cluster.np),
+				 error('IsConsistent error message: number of processors should not be NaN!');
+			 end
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,md) % {{{1
+		 
+			 %retrieve parameters
+			 modelname=md.name;
+			 analysis_type=md.analysis_type;
+			 mem_debug=md.mem_debug;
+
+			 %open file for writing: 
+			 fid=fopen([modelname '.queue'],'w');
+
+			 %write instructions for launching a job on the cluster
+			 fprintf(fid,'#!/bin/sh\n');
+			 if mem_debug==0,
+				 fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock  2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
+			 else
+				 %fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock  2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
+				 fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock  2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
+			 end
+
+			 if md.gprof,
+				 fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
+			 end
+
+			 if ~md.io_gather,
+				 %concatenate the output files:
+				 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+
+			 %close file
+			 fclose(fid);
+
+		 end
+		 %}}}
+		 function LaunchQueueJob(cluster,md,options)% {{{1
+			 
+			 %lauch command, to be executed via ssh
+			 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ...
+			                ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz  && source  ' md.name '.queue '];
+
+			if ~strcmpi(options.batch,'yes'),
+				
+				%compress the files into one zip.
+				compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue '  md.name '.petsc '];
+				if md.qmu_analysis,
+					compressstring=[compressstring md.name '.qmu.in'];
+				end
+				system(compressstring);
+				
+				disp('uploading input file and queueing script');
+				issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.runtimename '.tar.gz']});
+
+				disp('launching solution sequence on remote cluster');
+				issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+			else
+				disp('batch mode requested: not launching job interactively');
+				disp('launch solution sequence on remote cluster by hand');
+			end
+
+		 end %}}}
+		 function Download(cluster,md)% {{{1
+
+			%some check
+			if isempty(md.runtimename),
+				error('pfe Download error message: supply runtime name for results to be loaded!');
+			end
+
+			%Figure out the  directory where all the files are in: 
+			directory=[cluster.executionpath '/' md.runtimename '/'];
+
+			%What packages are we picking up from remote cluster
+			packages={[md.name '.outlog'],[md.name '.errlog']};
+			if md.qmu_analysis,
+				packages{end+1}=[md.name '.qmu.err'];
+				packages{end+1}=[md.name '.qmu.out'];
+				if isfield(md.qmu_params,'tabular_graphics_data'),
+					if md.qmu_params.tabular_graphics_data==true,
+						packages{end+1}='dakota_tabular.dat'; 
+					end
+				end
+			else
+				packages{end+1}=[md.name '.outbin'];
+			end
+
+			%copy files from cluster to present directory
+			issmscpin(cluster.name, cluster.login, cluster.port, directory, packages);
+		end %}}}
+	end
+end