Index: /issm/trunk-jpl/src/m/classes/clusters/vilje.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/vilje.m	(revision 22053)
+++ /issm/trunk-jpl/src/m/classes/clusters/vilje.m	(revision 22054)
@@ -1,3 +1,3 @@
-%PFE class definition
+%vilje class definition
 %
 %   Usage:
@@ -7,183 +7,179 @@
 
 classdef vilje
-    properties (SetAccess=public)  
-		 % {{{
-     name           = 'vilje';
-		 login          = '';
-		 numnodes       = 2;
-		 cpuspernode    = 32;
-     procspernodes  = 16;
-     mem            = 28;
-		 queue          = 'workq';
-		 time           = 2*60;
-		 codepath       = '';
-		 executionpath  = '';
-		 interactive    = 0;
-     port           = [];
-     accountname    = '';
+	properties (SetAccess=public)  
+		% {{{
+		name           = 'vilje';
+		login          = '';
+		numnodes       = 2;
+		cpuspernode    = 32;
+		procspernodes  = 16;
+		mem            = 28;
+		queue          = 'workq';
+		time           = 2*60;
+		codepath       = '';
+		executionpath  = '';
+		interactive    = 0;
+		port           = [];
+		accountname    = '';
+		% }}}
+	end
+	methods
+		function cluster=vilje(varargin) % {{{
 
-	 end
-	 properties (SetAccess=private) 
-		 np=numnodes*procspernodes;
-		 % }}}
-	 end
-	 methods
-		 function cluster=vilje(varargin) % {{{
+			%initialize cluster using default settings if provided
+			if (exist('vilje_settings')==2), vilje_settings; end
 
-			 %initialize cluster using default settings if provided
-			 if (exist('vilje_settings')==2), vilje_settings; end
+			%use provided options to change fields
+			cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
+		end
+		%}}}
+		function disp(cluster) % {{{
+			%  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('    accountname: %s',cluster.accountname));
+			disp(sprintf('    numnodes: %i',cluster.numnodes));
+			disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			disp(sprintf('    np: %i', cluster.cpuspernode*cluster.numnodes));
+			disp(sprintf('    procspernodes: %i',cluster.procspernodes));
+			disp(sprintf('    queue: %s',cluster.queue));
+			disp(sprintf('    codepath: %s',cluster.codepath));
+			disp(sprintf('    executionpath: %s',cluster.executionpath));
+			disp(sprintf('    interactive: %i',cluster.interactive));
+			disp(sprintf('    time: %i',cluster.time));
+			disp(sprintf('    memory: %i',cluster.mem));
+		end
+		%}}}
+		function md = checkconsistency(cluster,md,solution,analyses) % {{{
 
-			 %use provided options to change fields
-			 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
-		 end
-		 %}}}
-		 function disp(cluster) % {{{
-			 %  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('    accountname: %s',cluster.accountname));
-			 disp(sprintf('    numnodes: %i',cluster.numnodes));
-			 disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
-			 disp(sprintf('    np: %i', cluster.cpuspernode*cluster.numnodes));
-			 disp(sprintf('    procspernodes: %i',cluster.procspernodes));
-			 disp(sprintf('    queue: %s',cluster.queue));
-			 disp(sprintf('    codepath: %s',cluster.codepath));
-			 disp(sprintf('    executionpath: %s',cluster.executionpath));
-			 disp(sprintf('    interactive: %i',cluster.interactive));
-			 disp(sprintf('    time: %i',cluster.time));
-			 disp(sprintf('    memory: %i',cluster.mem));
-		 end
-		 %}}}
-		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+			available_queues={'workq'};
+			queue_requirements_time=[5*24*60];
+			queue_requirements_np=[30];
 
-			 available_queues={'workq'};
-			 queue_requirements_time=[5*24*60];
-			 queue_requirements_np=[30];
+			QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1)
 
-			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1)
+			%Miscelaneous
+			if isempty(cluster.login), md = checkmessage(md,'login empty'); end
+			if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end
+			if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end
+			if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
 
-			 %Miscelaneous
-			 if isempty(cluster.login), md = checkmessage(md,'login empty'); end
-       if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end
-			 if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end
-			 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+		end
+		%}}}
+		function numprocs=np(self) % {{{
+			%compute number of processors
+			numprocs=self.numnodes*self.cpuspernode;
+		end
+		%}}}
+		function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
 
-		 end
-		 %}}}
-		 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+			if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
 
-			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
-			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+			%compute number of processors
+			cluster.np=cluster.numnodes*cluster.cpuspernode;
 
-			 %compute number of processors
-			 cluster.np=cluster.numnodes*cluster.cpuspernode;
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+			fprintf(fid,'#PBS -S /bin/bash\n');
+			fprintf(fid,'#PBS -N %s\n',modelname);
+			fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,16);
+			fprintf(fid,'#PBS -l walltime=%s\n',cluster.time); %walltime is in seconds.
+			fprintf(fid,'#PBS -A %s\n',cluster.accountname);
+			fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+			fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
+			fprintf(fid,'mpiexec_mpt -n %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+			if ~io_gather, %concatenate the output files:
+				fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			end
+			fclose(fid);
+		end
+		%}}}
+		function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
 
-			 %write queuing script 
-			 fid=fopen([modelname '.queue'],'w');
-			 fprintf(fid,'#PBS -S /bin/bash\n');
-			 fprintf(fid,'#PBS -N %s\n',modelname);
-       fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,16);
-       fprintf(fid,'#PBS -l walltime=%s\n',cluster.time); %walltime is in seconds.
-       fprintf(fid,'#PBS -A %s\n',cluster.accountname);
-			 fprintf(fid,'#PBS -o %s.outlog \n',modelname);
-			 fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
-			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
-			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
-			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
-			 fprintf(fid,'mpiexec_mpt -n %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
-			 if ~io_gather, %concatenate the output files:
-				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
-			 end
-			 fclose(fid);
-		 end
-		 %}}}
-		 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+			if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
 
-			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
-			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+			executable='issm.exe';
+			if isdakota,
+				version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
+				if (version>=6),
+					executable='issm_dakota.exe';
+				end
+			end
+			if isoceancoupling,
+				executable='issm_ocean.exe';
+			end
 
-			 executable='issm.exe';
-			 if isdakota,
-				 version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
-				 if (version>=6),
-					 executable='issm_dakota.exe';
-				 end
-			 end
-			 if isoceancoupling,
-				 executable='issm_ocean.exe';
-			 end
+			%compute number of processors
+			cluster.np=cluster.numnodes*cluster.cpuspernode;                     
+			shortname = substring(modelname,1,min(12,length(modelname)));
 
-			 %compute number of processors
-			 cluster.np=cluster.numnodes*cluster.cpuspernode;                     
-       shortname = substring(modelname,1,min(12,length(modelname)));
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+			fprintf(fid,'#PBS -S /bin/bash\n');
+			fprintf(fid,'#PBS -N %s\n',shortname);
+			fprintf(fid,'#PBS -q %s \n',cluster.queue);
+			fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,cluster.procspernodes);
+			fprintf(fid,'#PBS -l walltime=%s\n',duration(0,cluster.time,0)); %walltime is in minutes.
+			fprintf(fid,'#PBS -A %s\n',cluster.accountname);
+			fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]);
+			fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]);
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
 
-			 %write queuing script 
-			 fid=fopen([modelname '.queue'],'w');
-			 fprintf(fid,'#PBS -S /bin/bash\n');
-			 fprintf(fid,'#PBS -N %s\n',shortname);
-			 fprintf(fid,'#PBS -q %s \n',cluster.queue);
-       fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,cluster.procspernodes);
-			 fprintf(fid,'#PBS -l walltime=%s\n',duration(0,cluster.time,0)); %walltime is in minutes.
-       fprintf(fid,'#PBS -A %s\n',cluster.accountname);
-			 fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]);
-			 fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]);
-			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
-			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
-			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
-       fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+			if ~io_gather, %concatenate the output files:
+				fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			end
+			fclose(fid);
 
-			 if ~io_gather, %concatenate the output files:
-				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
-			 end
-			 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,solution,[cluster.executionpath '/' dirname],modelname);
+				if ~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 UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
 
-			 %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,solution,[cluster.executionpath '/' dirname],modelname);
-				 if ~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 %}}}
+			%compress the files into one zip.
+			compressstring=['tar -zcf ' dirname '.tar.gz '];
+			for i=1:numel(filelist),
+				compressstring = [compressstring ' ' filelist{i}];
+			end
+			system(compressstring);
+			disp('uploading input file and queueing script');
+			directory=cluster.executionpath;
+			issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
 
+		end
+		%}}}
+		function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
 
-		 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
+			disp('launching solution sequence on remote cluster');
+			launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+				' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && qsub ' modelname '.queue '];
+			issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+		end %}}}
+		function Download(cluster,dirname,filelist)% {{{
 
-			 %compress the files into one zip.
-			 compressstring=['tar -zcf ' dirname '.tar.gz '];
-			 for i=1:numel(filelist),
-				 compressstring = [compressstring ' ' filelist{i}];
-			 end
-			 system(compressstring);
-			 disp('uploading input file and queueing script');
-			 directory=cluster.executionpath;
-			 issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
+			%copy files from cluster to current directory
+			directory=[cluster.executionpath '/' dirname '/'];
+			issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
 
-		 end
-		 %}}}
-
-
-		 function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
-
-			 disp('launching solution sequence on remote cluster');
-			  launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
-											 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && qsub ' modelname '.queue '];
-			 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
-		 end %}}}
-
-		 function Download(cluster,dirname,filelist)% {{{
-
-			 %copy files from cluster to current directory
-			 directory=[cluster.executionpath '/' dirname '/'];
-			 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
-
-		 end %}}}
+		end %}}}
 	end
 end