Index: /issm/trunk-jpl/src/m/classes/clusters/tetralith.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/tetralith.m	(revision 23265)
+++ /issm/trunk-jpl/src/m/classes/clusters/tetralith.m	(revision 23265)
@@ -0,0 +1,216 @@
+%teralith class definition
+%
+%   Usage:
+%      cluster=tetralith();
+%      cluster=tetralith('np',3);
+%      cluster=tetralith('np',3,'login','username');
+
+classdef tetralith
+	properties (SetAccess=public)  
+		% {{{
+		name           = 'tetralith';
+		login          = '';
+		numnodes       = 2;
+		cpuspernode    = 32;
+		mem            = 2000; %MB
+		queue          = 'normal';
+		time           = 2*60; %[minutes]
+		codepath       = '';
+		executionpath  = '';
+		interactive    = 0;
+		port           = [];
+		accountname    = '';
+		% }}}
+	end
+	methods
+		function cluster=tetralith(varargin) % {{{
+
+			%initialize cluster using default settings if provided
+			if (exist('tetralith_settings')==2), tetralith_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('    accountname: %s',cluster.accountname));
+			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('    codepath: %s',cluster.codepath));
+			disp(sprintf('    executionpath: %s',cluster.executionpath));
+			disp(sprintf('    interactive: %i',cluster.interactive));
+			disp(sprintf('    time: %i',cluster.time));
+			disp(sprintf('    memory: %i',cluster.mem));
+		end
+		%}}}
+		function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			available_queues={'normal','devel'};
+			queue_requirements_time=[7*24*60 60]; 
+			queue_requirements_np=[1024 2*32];
+
+			QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1)
+
+			%Miscelaneous
+			if isempty(cluster.login), md = checkmessage(md,'login empty'); end
+			if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end
+			if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end
+			if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+
+		end
+		%}}}
+		function numprocs=np(self) % {{{
+			%compute number of processors
+			numprocs=self.numnodes*self.cpuspernode;
+		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
+
+			%compute number of processors
+% 			cluster.np=cluster.numnodes*cluster.cpuspernode;
+			np(cluster);%=cluster.numnodes*cluster.cpuspernode;
+
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+			fprintf(fid,'#!/bin/bash\n');
+			fprintf(fid,'#\n');
+			fprintf(fid,'#SBATCH --job-name=%s\n',modelname);
+% 			fprintf(fid,'#SBATCH -p %s \n',cluster.partition);
+			fprintf(fid,'#SBATCH -A %s \n',cluster.accountname);
+% 			fprintf(fid,'#SBATCH --mail-type=ALL\n');
+			fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode);
+			%calculate walltime in hh:mm:ss format
+			walltime=datestr(cluster.time/(60*24),'HH:MM:SS')
+			fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss
+			fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem);
+			fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname);
+% 			fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith
+% 			fprintf(fid,'module load mpt/2.14\n')
+% 			fprintf(fid,'module load petsc/3.7.4d\n')
+% 			fprintf(fid,'module load parmetis/4.0.3\n') 
+% 			fprintf(fid,'module load mumps/5.0.2\n')
+% 			fprintf(fid,'export ISSM_DIR="%s"\n',cluster.codepath); %FIXME
+			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,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+% 			fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+			 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+% 			fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,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);
+		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
+
+			%compute number of processors
+% 			cluster.np=cluster.numnodes*cluster.cpuspernode;
+			np(cluster);%=cluster.numnodes*cluster.cpuspernode;                     
+% 			shortname = substring(modelname,1,min(12,length(modelname)));
+
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+			fprintf(fid,'#!/bin/bash\n');
+			fprintf(fid,'#\n');
+			fprintf(fid,'#SBATCH --job-name=%s\n',modelname);
+% 			fprintf(fid,'#SBATCH -p %s \n',cluster.partition);
+			fprintf(fid,'#SBATCH -A %s \n',cluster.accountname);
+% 			fprintf(fid,'#SBATCH --mail-type=ALL\n');
+			fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode);
+			%calculate walltime in hh:mm:ss format
+			walltime=datestr(cluster.time/(60*24),'HH:MM:SS');
+			fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss
+			fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem);
+			fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname);
+% 			fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith
+% 			fprintf(fid,'module load mpt/2.14\n')
+% 			fprintf(fid,'module load petsc/3.7.4d\n')
+% 			fprintf(fid,'module load parmetis/4.0.3\n') 
+% 			fprintf(fid,'module load mumps/5.0.2\n')
+			fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+% 			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,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+			 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+% 			fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+% 			fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,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,'mpiexec_mpt -np %i %s/issm.exe %s %s %s\n',cluster.np,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
+			system(compressstring);
+			disp('uploading input file and queueing script');
+			directory=cluster.executionpath;
+% 			issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
+			issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']});
+
+		end
+		%}}}
+		function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+
+			disp('launching solution sequence on remote cluster');
+			launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+				' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && sbatch ' modelname '.queue '];
+
+			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