Index: /issm/trunk-jpl/src/m/classes/clusters/localpfe.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/localpfe.m	(revision 21764)
+++ /issm/trunk-jpl/src/m/classes/clusters/localpfe.m	(revision 21764)
@@ -0,0 +1,239 @@
+%localpfe cluster class definition
+%
+%   Usage:
+%      cluster=localpfe('name','astrid','np',3);
+%      cluster=localpfe('name',oshostname(),'np',3,'login','username');
+
+classdef localpfe
+	properties (SetAccess=public) 
+		% {{{
+		name          = '';
+		login         = '';
+		np            = 1;
+		port          = 0;
+		interactive   = 1;
+		codepath      = [IssmConfig('ISSM_PREFIX') '/bin'];
+		etcpath       = [issmdir() '/etc'];
+		executionpath = [issmdir() '/execution'];
+		valgrind      = [issmdir() '/externalpackages/valgrind/install/bin/valgrind'];
+		valgrindlib   = [issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
+		valgrindsup   = [issmdir() '/externalpackages/valgrind/issm.supp'];
+		verbose       = 1;
+		shell         = '/bin/sh';
+		%}}}
+	end
+	methods
+		function cluster=localpfe(varargin) % {{{
+
+			%Change the defaults if ispc
+			if ispc,
+				cluster.codepath      = [issmdir() '\bin'];
+				cluster.etcpath       = [issmdir() '\etc'];
+				cluster.executionpath = [issmdir() '\execution'];
+			end
+
+			%use provided options to change fields
+			options=pairoptions(varargin{:});
+
+			%get name
+			cluster.name=getfieldvalue(options,'name',oshostname());
+
+			%initialize cluster using user settings if provided
+			if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
+
+			%OK get other 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('    np: %i',cluster.np));
+			disp(sprintf('    port: %i',cluster.port));
+			disp(sprintf('    codepath: %s',cluster.codepath));
+			disp(sprintf('    executionpath: %s',cluster.executionpath));
+			disp(sprintf('    etcpath: %s',cluster.etcpath));
+			disp(sprintf('    valgrind: %s',cluster.valgrind));
+			disp(sprintf('    valgrindlib: %s',cluster.valgrindlib));
+			disp(sprintf('    valgrindsup: %s',cluster.valgrindsup));
+			disp(sprintf('    verbose: %s',cluster.verbose));
+			disp(sprintf('    shell: %s',cluster.shell));
+		end
+		%}}}
+		function md = checkconsistency(cluster,md,solution,analyses) % {{{
+			if cluster.np<1
+				md = checkmessage(md,['number of processors should be at least 1']);
+			end
+			if isnan(cluster.np),
+				md = checkmessage(md,'number of processors should not be NaN!');
+			end
+		end
+		%}}}
+		function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
+
+			%write queuing script 
+			%what is the executable being called? 
+			executable='issm.exe';
+			if isdakota,
+				version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
+				if (version>=6),
+					executable='issm_dakota.exe';
+				end
+			end
+
+			fid=fopen([modelname '.queue'],'w');
+			fprintf(fid,'#!%s\n',cluster.shell);
+			fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname);
+			fclose(fid);
+
+
+			%in interactive mode, create a run file, and errlog and outlog file
+			if cluster.interactive,
+				fid=fopen([modelname '.errlog'],'w'); fclose(fid);
+				fid=fopen([modelname '.outlog'],'w'); fclose(fid);
+			end
+		end
+		%}}}
+		function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{
+		
+			%some checks: 
+			if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end
+
+			%what is the executable being called? 
+			executable='issm_slr.exe';
+
+			if ispc(), error('BuildQueueScriptMultipleModels not support yet on windows machines');end;
+			
+			%write queuing script 
+			fid=fopen([modelname '.queue'],'w');
+			
+			fprintf(fid,'#!%s\n',cluster.shell);
+
+			%number of cpus: 
+			mpistring=sprintf('mpiexec -np %i ',cluster.np);
+
+			%executable: 
+			mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)];
+			
+			%solution name: 
+			mpistring=[mpistring sprintf('%s ',solution)];
+
+			%execution directory and model name: 
+			mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)];
+
+			%inform main executable of how many icecaps, glaciers and earth models are being run: 
+			mpistring=[mpistring sprintf(' %i ',length(dirnames))];
+			
+			%icecaps, glaciers and earth location, names and number of processors associated:
+			for i=1:length(dirnames),
+			mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})];
+			end
+
+			%log files: 
+			if ~cluster.interactive,
+				mpistring=[mpistring sprintf('2> %s.errlog> %s.outlog',modelname,modelname)];
+			end
+
+			%write this long string to disk: 
+			fprintf(fid,mpistring);
+			fclose(fid);
+
+			%in interactive mode, create a run file, and errlog and outlog file
+			if cluster.interactive,
+				fid=fopen([modelname '.errlog'],'w'); fclose(fid);
+				fid=fopen([modelname '.outlog'],'w'); fclose(fid);
+			end
+		end
+		%}}}
+		function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+
+			%write queuing script 
+			if ~ispc(),
+
+				fid=fopen([modelname '.queue'],'w');
+				fprintf(fid,'#!/bin/sh\n');
+				if ~isvalgrind,
+					if cluster.interactive
+						fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+					else
+						fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
+					end
+				elseif isgprof,
+					fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
+				else
+					%Add --gen-suppressions=all to get suppression lines
+					fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
+					fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
+						cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
+				end
+				if ~io_gather, %concatenate the output files:
+					fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
+				end
+				fclose(fid);
+
+			else % Windows
+
+				fid=fopen([modelname '.bat'],'w');
+				fprintf(fid,'@echo off\n');
+				if cluster.interactive
+					fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname);
+				else
+					fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
+						cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
+				end
+				fclose(fid);
+			end
+
+			%in interactive mode, create a run file, and errlog and outlog file
+			if cluster.interactive,
+				fid=fopen([modelname '.errlog'],'w'); fclose(fid);
+				fid=fopen([modelname '.outlog'],'w'); fclose(fid);
+			end
+		end
+		%}}}
+		function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
+			if ~ispc,
+
+				%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);
+
+				if cluster.verbose, disp('uploading input file and queueing script'); end
+				issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+			end
+		end %}}}
+		function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+
+			%figure out what shell extension we will use:
+			if isempty(strfind(cluster.shell,'csh')),
+				shellext='sh';
+			else
+				shellext='csh';
+			end
+
+			if cluster.verbose, disp('launching solution sequence on remote cluster'); end
+
+			launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && rm -rf ADOLC* && tar -zxf ' dirname '.tar.gz  && rm -rf *.tar.gz'];
+			issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+
+		end %}}}
+		function Download(cluster,dirname,filelist)% {{{
+
+			if ispc(),
+				%do nothing
+				return;
+			end
+
+			%copy files from cluster to current directory
+			issmscpin(cluster.name,cluster.login,cluster.port,cluster.executionpath,filelist);
+		end %}}}
+	end
+end