Index: sm/trunk-jpl/bin/vilje.m
===================================================================
--- /issm/trunk-jpl/bin/vilje.m	(revision 19962)
+++ 	(revision )
@@ -1,173 +1,0 @@
-%PFE class definition
-%
-%   Usage:
-%      cluster=greenplanet();
-%      cluster=greenplanet('np',3);
-%      cluster=greenplanet('np',3,'login','username');
-
-classdef greenplanet
-    properties (SetAccess=public)  
-		 % {{{
-		 name          = 'vilje'
-		 login         = '';
-                 accountname    ='';
-		 numnodes      = 20;
-		 cpuspernode   = 8;
-		 port          = 8000;
-		 queue         = '';
-		 codepath      = '';
-		 executionpath = '';
-		 interactive   = 0;
-		 time          = 24*60;
-		 memory        = 2;
-	 end
-	 properties (SetAccess=private) 
-		 np=20*8;
-		 % }}}
-	 end
-	 methods
-		 function cluster=vilje(varargin) % {{{
-
-			 %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('    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));
-			 disp(sprintf('    time: %i',cluster.time));
-			 disp(sprintf('    memory: %i',cluster.memory));
-		 end
-		 %}}}
-		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
-
-			 available_queues={'c6145','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), 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 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
-
-			 %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:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor);
-                         fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds.
-                         fprintf(fid,'#PBS -A %s\n',cluster.accountname);
-			 fprintf(fid,'#PBS -q %s \n',cluster.queue);
-			 fprintf(fid,'#PBS -l mem=%igb\n',cluster.memory);
-%			 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,'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 -np %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) % {{{
-
-			 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;
-
-			 %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 -q %s \n',cluster.queue);
-                         fprintf(fid,'#PBS -l select=%i:ncpus=%i:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor);
-			 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds.
-                         fprintf(fid,'#PBS -A %s\n',cluster.accountname);
-			 fprintf(fid,'#PBS -l mem=%igb\n',cluster.memory);
-%			 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,'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/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
-			 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,EnumToString(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 LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
-
-			 %compress the files into one zip.
-			 compressstring=['tar -zcf ' dirname '.tar.gz '];
-			 for i=1:numel(filelist),
-				 compressstring = [compressstring ' ' filelist{i}];
-			 end
-			 if cluster.interactive,
-				 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
-			 end
-			 system(compressstring);
-
-			 disp('uploading input file and queueing script');
-			 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
-
-			 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