Index: /issm/trunk-jpl/src/m/classes/clusters/andes.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/andes.m	(revision 28246)
+++ /issm/trunk-jpl/src/m/classes/clusters/andes.m	(revision 28246)
@@ -0,0 +1,175 @@
+%ANDES (Dartmouth) cluster class definition
+%
+%   Usage:
+%      cluster=andes();
+%      cluster=andes('np',3);
+%      cluster=andes('np',3,'login','username');
+
+classdef andes
+	properties (SetAccess=public)
+		% {{{
+		name          = 'andes'
+		login         = '';
+		numnodes      = 1;
+		cpuspernode   = 16;
+		codepath      = '';
+		executionpath = '';
+		interactive   = 0;
+		time          = 10; %in hours
+		memory        = 2;  %in Gb
+		email         = 'END,FAIL';
+		deleteckptdata= 0;
+	end
+	%}}}
+	methods
+		function cluster=andes(varargin) % {{{
+
+			%initialize cluster using default settings if provided
+			if (exist('andes_settings')==2), andes_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('    numnodes:    %i',cluster.numnodes));
+			disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			disp(sprintf('    time: %i hours',cluster.time));
+			disp(sprintf('    memory: %i Gb',cluster.memory));
+			disp(sprintf('    email: %s (notifications: BEGIN,END,FAIL)',cluster.email));
+			disp(sprintf('    deleteckptdata: %i',cluster.deleteckptdata));
+			disp(sprintf('    codepath:      %s',cluster.codepath));
+			disp(sprintf('    executionpath: %s',cluster.executionpath));
+			disp(sprintf('    interactive: %i',cluster.interactive));
+		end
+		%}}}
+		function numprocs=nprocs(cluster) % {{{
+			%compute number of processors
+			numprocs=cluster.numnodes*cluster.cpuspernode;
+		end
+		%}}}
+		function md = checkconsistency(cluster,md,solution,analyses) % {{{
+			%Miscellaneous
+			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 BuildKrigingQueueScript(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,'#SBATCH --job-name=%s\n',modelname);
+			fprintf(fid,'#SBATCH --account=ice\n'); %Make sure we use the ICE account for this run
+			fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			fprintf(fid,'#SBATCH -e %s.errlog \n',modelname);
+			fprintf(fid,'#SBATCH --nodes=%i\n',cluster.numnodes);
+			fprintf(fid,'#SBATCH --ntasks-per-node=%i\n',cluster.cpuspernode);
+			fprintf(fid,'#SBATCH --time=%s\n',datestr(cluster.time/24,'HH:MM:SS')); %walltime is in HH:MM:SS format. cluster.time is in hour
+			fprintf(fid,'#SBATCH --mem=%iG\n',cluster.memory);
+			if ~isempty(cluster.email)
+				fprintf(fid,'#SBATCH --mail-type=%s\n',cluster.email);
+			end
+			fprintf(fid,'\n');
+
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');      
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			fprintf(fid,'srun %s/kriging.exe %s %s\n', 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,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,'#SBATCH --job-name=%s\n',modelname);
+			fprintf(fid,'#SBATCH --account=ice\n'); %Make sure we use the ICE account for this run
+			fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			fprintf(fid,'#SBATCH -e %s.errlog \n',modelname);
+			fprintf(fid,'#SBATCH --nodes=%i\n',cluster.numnodes);
+			fprintf(fid,'#SBATCH --ntasks-per-node=%i\n',cluster.cpuspernode);
+			fprintf(fid,'#SBATCH --time=%s\n',eraseBetween(datestr(cluster.time/24,'dd-HH:MM:SS'),1,1)); %walltime is in d-HH:MM:SS format. cluster.time is in hour
+			fprintf(fid,'#SBATCH --mem=%iG\n',cluster.memory);
+			if ~isempty(cluster.email)
+				fprintf(fid,'#SBATCH --mail-type=%s\n',cluster.email);
+			end
+			fprintf(fid,'\n');
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			fprintf(fid,'mpirun -n %i %s/issm.exe %s %s %s\n',cluster.nprocs(), cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+			if ~io_gather, %concatenate the output files:
+				fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			end
+
+			if (cluster.deleteckptdata)
+				fprintf(fid,'rm -rf *.rst *.ckpt\n');
+			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,'mpirun -n %i %s/issm.exe %s %s %s\n',cluster.nprocs(), cluster.codepath,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 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
+			if cluster.interactive,
+				compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
+			end
+			system(compressstring);
+
+			disp('uploading input file and queuing script');
+			issmscpout(cluster.name,cluster.executionpath,cluster.login,0,{[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 && sbatch ' modelname '.queue '];
+			else
+				launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+					' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && sbatch ' modelname '.queue '];
+			end
+			issmssh(cluster.name,cluster.login,0,launchcommand);
+		end %}}}
+		function Download(cluster,dirname,filelist) % {{{
+
+			%copy files from cluster to current directory
+			directory=[cluster.executionpath '/' dirname '/'];
+			issmscpin(cluster.name,cluster.login,0,directory,filelist);
+
+		end %}}}
+	end
+end