Index: /issm/trunk-jpl/src/m/classes/clusters/yellowstone.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/yellowstone.m	(revision 21699)
+++ /issm/trunk-jpl/src/m/classes/clusters/yellowstone.m	(revision 21699)
@@ -0,0 +1,156 @@
+%YELLOWSTONE class definition
+%
+%   Usage:
+%      cluster=yellowstone();
+%      cluster=yellowstone('np',3);
+%      cluster=yellowstone('np',3,'login','username');
+
+classdef yellowstone
+    properties (SetAccess=public)  
+		 % {{{
+		 name           = 'yellowstone.ucar.edu'
+		 login          = '';
+		 modules        = {'ncarenv/1.0' 'ncarbinlibs/1.1' 'perlmods/5.0' 'gmake/4.1' 'python/2.7.7' 'all-python-libs' 'git/2.3.0' 'intel/15.0.3' 'mkl/11.1.2' 'esmf' 'esmf-6.3.0rp1-defio-mpi-O' 'netcdf-mpi/4.3.3.1' 'pnetcdf/1.6.1' 'ncarcompilers/1.0' 'cmake/3.0.2' 'matlab/R2015b' 'issm'};
+		 numnodes       = 1;
+		 cpuspernode    = 8;
+		 port           = 0;
+		 queue          = 'premium';
+		 time           = 12*60;
+		 processor      = 'sandy';
+		 codepath       = '';
+		 executionpath  = '';
+		 grouplist     = 'P93300301';
+	 end
+	 %}}}
+	 methods
+		 function cluster=yellowstone(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('yellowstone_settings')==2), yellowstone_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));
+			 modules=''; for i=1:length(cluster.modules), modules=[modules cluster.modules{i} ',']; end; modules=modules(1:end-1); 
+			 disp(sprintf('    modules: %s',modules));
+			 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('    time: %i',cluster.time));
+			 disp(sprintf('    processor: %s',cluster.processor));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    grouplist: %s',cluster.grouplist));
+		 end
+		 %}}}
+		 function numprocs=np(cluster) % {{{
+			 %compute number of processors
+			 numprocs=cluster.numnodes*cluster.cpuspernode;
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'premium','regular'};
+			 queue_requirements_time=[12*60 12*650];
+			 queue_requirements_np=[16384 16384];
+
+			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time)
+
+			 %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
+			 if isempty(cluster.grouplist), md = checkmessage(md,'grouplist empty'); end
+
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+
+			 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/tcsh\n');
+			 fprintf(fid,'#BSUB -P %s\n',cluster.grouplist);
+			 fprintf(fid,'#BSUB -W %i:%i\n',floor(cluster.time/60),cluster.time-floor(cluster.time/60)*60);
+			 fprintf(fid,'#BSUB -n %i\n',cluster.np);
+			 fprintf(fid,'#BSUB -J %s\n',modelname);
+			 fprintf(fid,'#BSUB -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]);
+			 fprintf(fid,'#BSUB -e %s.errlog \n',[cluster.executionpath '/' dirname '/' modelname]);
+			 fprintf(fid,'#BSUB -q %s\n',cluster.queue);
+
+			 fprintf(fid,'module purge\n');
+			 for i=1:length(cluster.modules),
+				 fprintf(fid,'module load %s\n',cluster.modules{i});
+			 end
+
+			 fprintf(fid,'setenv OMP_STACKSIZE 256M\n');
+			 fprintf(fid,'setenv MP_LABELIO yes\n');
+			 fprintf(fid,'setenv MP_INFOLEVEL 2\n');
+			 fprintf(fid,'setenv MP_SHARED_MEMORY yes\n');
+			 fprintf(fid,'setenv MP_EUILIB us\n');
+			 fprintf(fid,'setenv MP_STDOUTMODE unordered\n');
+			 fprintf(fid,'setenv MP_RC_USE_LMC yes\n');
+			 fprintf(fid,'setenv MP_MPILIB mpich2\n');
+			 fprintf(fid,'setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/ibmhpc/pecurrent/mpich2/intel/lib64/\n');
+			 fprintf(fid,'setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/ncar/opt/intel/psxe-2015_update3/impi/5.0.3.048/lib64/\n');
+
+			 fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname);
+
+			 fprintf(fid,'mpirun.lsf %s/%s %s %s %s\n',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');
+			 directory=cluster.executionpath;
+
+			 issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']});
+
+		 end
+		 %}}}
+		 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+
+			 %lauch command, to be executed via ssh
+			 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+						 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && bsub < ' modelname '.queue '];
+
+			 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