Index: /issm/trunk-jpl/src/m/classes/clusters/localaurora.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/localaurora.m	(revision 23617)
+++ /issm/trunk-jpl/src/m/classes/clusters/localaurora.m	(revision 23617)
@@ -0,0 +1,115 @@
+%LOCALAURORA class definition
+%
+%   Usage:
+%      cluster=localaurora();
+%      cluster=localaurora('np',3);
+%      cluster=localaurora('np',3,'login','username');
+
+classdef localaurora
+    properties (SetAccess=public) 
+		 % {{{
+		 name='aurora'
+		 login='username';
+		 numnodes = 1;
+		 cpuspernode = 24;
+		 modules = {'intel/cluster-toolkit-2013.5.192'};
+		 port=1070;
+		 queue='shortq';
+		 time=3*60;
+		 codepath='~/issm/trunk/';
+		 executionpath='~/issm/trunk/execution/';
+		 mpipath='/opt/intel/impi/4.1.3/intel64/bin/';
+		 %}}}
+	 end
+	 methods
+		 function cluster=localaurora(varargin) % {{{
+			 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('    numnodes: %i',cluster.numnodes));
+			 disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			 disp(sprintf('    port: %i',cluster.port));
+			 disp(sprintf('    queue: %s',cluster.queue));
+			 disp(sprintf('    time: %i',cluster.time));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'debugq','shortq','mediumq','longq','verylongq'};
+			 queue_requirements_time=[60*1 60*3 60*12 60*48 60*192];
+			 queue_requirements_np=[16 256 256 128 128];
+
+			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.numnodes.*cluster.cpuspernode,cluster.time)
+		 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
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+			 fprintf(fid,'#!/bin/bash\n');
+			 fprintf(fid,'#PBS -l select=%i:ncpus=%i\n',cluster.numnodes,cluster.cpuspernode);
+			 fprintf(fid,'#PBS -N %s\n',modelname);
+			 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds.
+			 fprintf(fid,'#PBS -q %s\n',cluster.queue);
+			 fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+			 fprintf(fid,'#PBS -e %s.errlog \n',modelname);
+			 fprintf(fid,'source /usr/share/Modules/init/bash\n');
+			 for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n\n']); end
+			 fprintf(fid,'export PATH="$PATH:."\n\n');
+			 fprintf(fid,'export MPI_GROUP_MAX=64\n\n');
+			 fprintf(fid,'export MPI_UNBUFFERED_STDIO=true\n\n');
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);
+			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');      
+			 fprintf(fid,'export PATH="$PATH:.:%s"\n',cluster.mpipath);
+			 fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
+			 fprintf(fid,'cd $PBS_O_WORKDIR\n');
+			 fprintf(fid,'mpirun -n %i %s/issm.exe %s %s %s',cluster.numnodes*cluster.cpuspernode,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+			 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)% {{{
+
+			 if ~isempty(restart)
+				 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue '];
+			 else
+				 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+					 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && qsub ' modelname '.queue '];
+			 end
+
+			 disp('launching solution sequence on remote cluster');
+			 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