Index: /issm/trunk-jpl/src/m/classes/clusters/raijin.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/raijin.m	(revision 20686)
+++ /issm/trunk-jpl/src/m/classes/clusters/raijin.m	(revision 20686)
@@ -0,0 +1,125 @@
+%RAIJIN class definition
+%
+%   Usage:
+%      cluster=raijin();
+%      cluster=raijin('np',3);
+%      cluster=raijin('np',3,'login','username');
+
+classdef raijin
+    properties (SetAccess=public)  
+		 % {{{
+		 name='';
+		 login='';
+		 np=0;
+                 mem=0;
+                 time=0;
+                 project='';
+                 email='';
+		 port=0;
+		 queue='';
+		 codepath='';
+		 executionpath='';
+                 modules={};
+	 end
+	 %}}}
+	 methods
+		 function cluster=raijin(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('raijin_settings')==2), raijin_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('    port: %i',cluster.port));
+			 disp(sprintf('    mem: %i',cluster.mem));
+			 disp(sprintf('    time: %i',cluster.time));
+			 disp(sprintf('    np: %i',cluster.np));
+			 disp(sprintf('    queue: %s',cluster.queue));
+                         disp(sprintf('    project: %s',cluster.project));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'express', 'normal'};
+			 queue_requirements_time=[5*60 40*60];
+			 queue_requirements_np=[256 1024];
+
+			 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.codepath), md = checkmessage(md,'codepath empty'); end
+			 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
+                     
+			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+                         fprintf(fid,'#PBS -S /bin/bash\n');
+                         fprintf(fid,'#PBS -P %s\n', cluster.project);
+                         fprintf(fid,'#PBS -q %s\n',cluster.queue);
+                         fprintf(fid,'#PBS -l ncpus=%i\n',cluster.np);
+                         fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); % walltime is in seconds
+                         fprintf(fid,'#PBS -l mem=%igb\n', cluster.mem);
+                         fprintf(fid,'#PBS -M %s\n', cluster.email);
+                         fprintf(fid,'#PBS -o %s.outlog\n',(modelname));
+                         fprintf(fid,'#PBS -e %s.errlog\n',(modelname));
+                         fprintf(fid,'#PBS -l wd\n\n');
+                         fprintf(fid,'source ~/.bashrc\n');
+                         fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');
+                         for i=1:numel(cluster.modules)
+                             fprintf(fid,'module load %s\n', cluster.modules{i});
+                         end
+			 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);
+		 end %}}}
+		 function UploadQueueJob(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
+			 system(compressstring);
+
+			 disp('uploading input file and queueing script');
+			 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+
+		 end %}}}
+		 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+                         
+			 disp('launching solution sequence on remote cluster');
+			 if ~isempty(restart)
+				 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && qsub ' modelname '.queue '];
+			 else
+				 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+					 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && qsub ' modelname '.queue '];
+			 end
+			 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