Index: sm/trunk-jpl/src/m/classes/clusters/localaurora.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/localaurora.m	(revision 23624)
+++ 	(revision )
@@ -1,130 +1,0 @@
-%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 numprocs=np(cluster) % {{{
-			 %compute number of processors
-			 numprocs=cluster.numnodes*cluster.cpuspernode;
-		 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
-			 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
-
-			 %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/%s %s %s %s',cluster.np(),cluster.codepath,executable,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