Index: /issm/trunk-jpl/src/m/classes/clusters/frontera.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/frontera.m	(revision 26355)
+++ /issm/trunk-jpl/src/m/classes/clusters/frontera.m	(revision 26355)
@@ -0,0 +1,202 @@
+%FRONTERA cluster class definition
+%
+%   Usage:
+%      cluster=frontera();
+%      cluster=frontera('np',3);
+%      cluster=frontera('np',3,'login','username');
+
+classdef frontera
+	properties (SetAccess=public)
+		% {{{
+		name          = 'ls5.tacc.utexas.edu'
+		login         = '';
+		modules        = {'intel/18.0.2' 'gsl'};
+		numnodes      = 1;
+		cpuspernode   = 24;
+		port          = 1099;
+		queue         = 'normal';
+		codepath      = '';
+		executionpath = '';
+		interactive   = 0;
+		time          = 48*60*60;
+		email         = '';
+	end
+	%}}}
+	methods
+		function cluster=frontera(varargin) % {{{
+
+			%initialize cluster using default settings if provided
+			if (exist('frontera_settings')==2), frontera_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('    modules: %s',strjoin(cluster.modules,', ')));
+			disp(sprintf('    port: %i',cluster.port));
+			disp(sprintf('    numnodes: %i',cluster.numnodes));
+			disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			disp(sprintf('    np: %i',cluster.nprocs()));
+			disp(sprintf('    port: %i',cluster.port));
+			disp(sprintf('    queue: %s',cluster.queue));
+			disp(sprintf('    codepath: %s',cluster.codepath));
+			disp(sprintf('    executionpath: %s',cluster.executionpath));
+			disp(sprintf('    interactive: %i',cluster.interactive));
+			disp(sprintf('    time: %i',cluster.time));
+			disp(sprintf('    email: %s',cluster.email));
+		end
+		%}}}
+		function numprocs=nprocs(cluster) % {{{
+			%compute number of processors
+			numprocs=cluster.numnodes*cluster.cpuspernode;
+		end
+		%}}}
+		function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			%https://frontera-portal.tacc.utexas.edu/user-guide/running/
+			available_queues={'small','normal','development'};
+			queue_requirements_time=[48*60*60 48*60*60 2*60*60];
+			queue_requirements_np=[2*56 512*56 40*56];
+
+			QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.nprocs(),cluster.time)
+
+			%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,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+
+			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,'#$ -N %s\n',modelname);
+			fprintf(fid,'#$ -q %s \n',cluster.queue);
+			fprintf(fid,'#$ -pe one-node-mpi 2-64\n');
+			fprintf(fid,'#$ -R y\n');
+			fprintf(fid,'#$ -m beas\n');
+			fprintf(fid,'#$ -o %s.outlog \n',modelname);
+			fprintf(fid,'#$ -e %s.errlog \n\n',modelname);
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
+			fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.nprocs(),cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+			if ~io_gather, %concatenate the output files:
+				fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			end
+			fclose(fid);
+		end
+		%}}}
+		function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+
+			if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			executable='issm.exe';
+			if isdakota,
+				version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
+				if (version>=6),
+					executable='issm_dakota.exe';
+				end
+			end
+			if isoceancoupling,
+				executable='issm_ocean.exe';
+			end
+
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+
+			fprintf(fid,'#!/bin/bash\n');
+			fprintf(fid,'#SBATCH -J %s \n',modelname);
+			fprintf(fid,'#SBATCH -p %s \n',cluster.queue);
+			fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			fprintf(fid,'#SBATCH -e %s.errlog \n',modelname);
+			fprintf(fid,'#SBATCH -n %i \n',cluster.numnodes*max(cluster.nprocs()/cluster.numnodes,24));
+			fprintf(fid,'#SBATCH -N %i \n',cluster.numnodes);
+			fprintf(fid,'#SBATCH -t %02i:%02i:00 \n\n',floor(cluster.time/3600),floor(mod(cluster.time,3600)/60));
+			for i=1:numel(cluster.modules),
+				fprintf(fid,['module load ' cluster.modules{i} '\n']);
+			end
+
+			if isdakota,
+				fprintf(fid,'export KMP_AFFINITY="granularity=fine,compact,verbose" \n\n');
+			end
+
+			if length(find(cluster.email=='@'))>0
+				fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email);
+				fprintf(fid,'#SBATCH --mail-type=end \n\n');
+
+				%fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email);
+			end
+
+			fprintf(fid,'export PATH="$PATH:."\n\n');
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			fprintf(fid,'ibrun -np %i %s/%s %s %s %s\n',cluster.nprocs(),cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+			if ~io_gather, %concatenate the output files:
+				fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			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,'ibrun -np %i %s/%s %s %s %s\n',cluster.nprocs(),executable,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 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 && 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,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