Index: /issm/trunk-jpl/src/m/classes/clusters/greenplanet.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/greenplanet.m	(revision 11372)
+++ /issm/trunk-jpl/src/m/classes/clusters/greenplanet.m	(revision 11372)
@@ -0,0 +1,202 @@
+%PFE class definition
+%
+%   Usage:
+%      cluster=greenplanet();
+%      cluster=greenplanet('np',3);
+%      cluster=greenplanet('np',3,'login','username');
+
+classdef greenplanet
+    properties (SetAccess=public)  
+		 % {{{1
+		 name='greenplanet'
+		 login='';
+		 numnodes=20;
+		 cpuspernode=8; 
+		 port=8000;
+		 queue='rignot';
+		 codepath='';
+		 executionpath='';
+		 interactive=0;
+	 end
+	 properties (SetAccess=private) 
+		 np=20*8;
+		 % }}}
+	 end
+	 methods
+		 function cluster=greenplanet(varargin) % {{{1
+
+			 %initialize cluster using default settings if provided
+			 if (exist('greenplanet_settings')==2), greenplanet_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('greenplanet')),
+					 cluster.(fieldname)=fieldvalue;
+				 else
+					 disp(['''' fieldname ''' is not a property of cluster greenplanet']);
+				 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('    port: %i',cluster.port));
+			 disp(sprintf('    numnodes: %i',cluster.numnodes));
+			 disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			 disp(sprintf('    np: %i',cluster.cpuspernode*cluster.numnodes));
+			 disp(sprintf('    queue: %s',cluster.queue));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    interactive: %i',cluster.interactive));
+		 end
+		 %}}}
+		 function checkconsistency(cluster,md,solution,analyses) % {{{1
+
+			 available_queues={'rignot','default'};
+			 queue_requirements_time=[Inf Inf];
+			 queue_requirements_np=[80 80];
+
+			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1)
+
+			 %Miscelaneous
+			 if isempty(cluster.login), checkmessage('login empty'); end
+			 if isempty(cluster.codepath), checkmessage('codepath empty'); end
+			 if isempty(cluster.executionpath), checkmessage('executionpath empty'); end
+
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,md) % {{{1
+
+			 %retrieve parameters 
+			 modelname=md.miscellaneous.name; 
+			 solution=md.private.solution;
+			 isvalgrind=md.debug.valgrind;
+
+			 %compute number of processors
+			 cluster.np=cluster.numnodes*cluster.cpuspernode;
+
+			 %open file for writing: 
+			 fid=fopen([modelname '.queue'],'w');
+
+			 fprintf(fid,'#PBS -S /bin/bash\n');
+			 fprintf(fid,'#PBS -N %s\n',modelname);
+			 fprintf(fid,'#PBS -q %s \n',cluster.queue);
+			 fprintf(fid,'#PBS -l nodes=%i:ppn=%i\n',cluster.numnodes,cluster.cpuspernode);
+			 fprintf(fid,'#PBS -m bea\n');
+			 fprintf(fid,'#PBS -M mmorligh@uci.edu\n');
+			 fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+			 fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+
+			 fprintf(fid,'cd %s\n\n',cluster.executionpath);
+			 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+
+			 if ~md.settings.io_gather,
+				 %concatenate the output files:
+				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+
+			 %close file
+			 fclose(fid);
+
+			 %in interactive mode, create a run file, and errlog and outlog file
+			 if cluster.interactive,
+				 fid=fopen([modelname '.run'],'w');
+				 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+
+				 if ~md.settings.io_gather,
+					 %concatenate the output files:
+					 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+				 end
+				 fclose(fid);
+				 fid=fopen([modelname '.errlog'],'w');
+				 fclose(fid);
+				 fid=fopen([modelname '.outlog'],'w');
+				 fclose(fid);
+			 end
+		 end %}}}
+		 function LaunchQueueJob(cluster,md,options)% {{{1
+			 
+			 %lauch command, to be executed via ssh
+			 if ~cluster.interactive, 
+				launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.private.runtimename ' && mkdir ' md.private.runtimename ...
+			                ' && cd ' md.private.runtimename ' && mv ../' md.private.runtimename '.tar.gz ./ && tar -zxf ' md.private.runtimename '.tar.gz  && qsub ' md.miscellaneous.name '.queue '];
+			else
+				launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive) ' && tar -zxf ' md.private.runtimename '.tar.gz'];
+			end
+
+			if ~strcmpi(options.batch,'yes'),
+				
+				%compress the files into one zip.
+				compressstring=['tar -zcf ' md.private.runtimename '.tar.gz ' md.miscellaneous.name '.bin ' md.miscellaneous.name '.queue '  md.miscellaneous.name '.petsc '];
+				if md.qmu.isdakota,
+					compressstring=[compressstring md.miscellaneous.name '.qmu.in '];
+				end
+				if cluster.interactive,
+					compressstring=[compressstring md.miscellaneous.name '.run ' md.miscellaneous.name '.errlog ' md.miscellaneous.name '.outlog '];
+				end
+				system(compressstring);
+				
+				disp('uploading input file and queueing script');
+				if cluster.interactive,
+					directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)];
+				else 
+					directory=cluster.executionpath;
+				end
+				
+				issmscpout(cluster.name,directory,cluster.login,cluster.port,{[md.private.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.private.runtimename),
+				if ~cluster.interactive,
+					error('greenplanet Download error message: supply runtime name for results to be loaded!');
+				end
+			end
+
+			%Figure out the  directory where all the files are in: 
+			if ~cluster.interactive,
+				directory=[cluster.executionpath '/' md.private.runtimename '/'];
+			else
+				directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive) '/'];
+			end
+
+			%What packages are we picking up from remote cluster
+			if ~cluster.interactive,
+				packages={[md.miscellaneous.name '.outlog'],[md.miscellaneous.name '.errlog']};
+			else
+				packages={};
+			end
+			if md.qmu.isdakota,
+				packages{end+1}=[md.miscellaneous.name '.qmu.err'];
+				packages{end+1}=[md.miscellaneous.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.miscellaneous.name '.outbin'];
+			end
+
+			%copy files from cluster to present directory
+			issmscpin(cluster.name, cluster.login, cluster.port, directory, packages);
+
+		end %}}}
+	end
+end